Aspergillus Kawachi Acid-Stable Alpha Amylase and Applications in Granular Starch Hydrolysis

ABSTRACT

The present invention relates to a method for producing an end product and particularly an alcohol which comprises contacting a granular starch substrate with an acid-stable alpha amylase (asAA) having granular starch hydrolyzing (GSH) activity and a glucoamylase (GA) in a fermentation step which also comprises ethanologenic microorganisms at a temperature between about 25 to 65° C. and producing an end-product.

The present application claims priority to U.S. Provisional PatentApplication Ser. No. 60/575,175, filed May 27, 2004; U.S. ProvisionalPatent Application Ser. No. 60/605,437, filed Aug. 30, 2004;International Application No. PCT/US04/040040, filed Nov. 30, 2004 andU.S. Provisional Patent Application Ser. No. 60/647,925 filed Jan. 28,2005, the contents of which are fully incorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates to an acid-stable alpha amylase (asAA)derived from a strain of Aspergillus kawachi, which has granular starchhydrolyzing (GSH) activity. Further the invention relates to theheterologous expression of an asAA having GSH activity in filamentousfungal host cells and particularly in Trichoderma and Aspergillus cellsand the use of asAA having GSH activity in compositions, whichoptionally include glucoamylases, to enhance starch hydrolysis andalcohol production.

BACKGROUND OF THE INVENTION

Glucoamylases, and particularly glucoamylases having granular starchhydrolyzing (GSH) activity are important industrial enzymes used forproducing products such as organic acids (i.e. lactic acids), aminoacids (i.e. glutamic acids), alcohols (i.e. ethanol) and other compoundsfrom starch substrates derived from plant based substrates, such asgrains and cereals. During microbial fermentations, and particularlyduring simultaneous saccharification and fermentation (SSF), it would beof benefit to reduce the amount of residual starch in the fermentationwhen granular starch substrates are used as a carbon feed. The presentinvention answers this need by providing an acid-stable alpha amylase(asAA) having granular starch hydrolyzing activity, which may be used incombination with a glucoamylase to enhance starch hydrolysis and alcoholproduction.

Additionally, benefits of the present invention over prior artcompositions and methods include one or more of the following: a) areduction of thermal energy use during starch hydrolysis and end-productproduction; b) reduction in the requirement of high enzyme dosage; c)utilization of a continuous release of glucose from starch to feed theyeast; d) maintenance of a relatively low glucose level in thefermenter, which significantly reduces the high risk of microbialcontamination and removes the catabolite repression of yeast due to highconcentration of free glucose; e) reduction in formation of browningreaction products; f) reduction or removal of calcium addition, whichwas required during the prior art jet cooking process; g) reduction inwater utilization during the fermentation process; h) use of highersolids content in the fermentation, which may result in higherend-product formation and reduced energy costs; i) reduced levels ofproduction of certain by-products, such as glycerol; and j) decreasedresidual starch content and increased protein content of distillers drygrains plus solubles.

SUMMARY OF THE INVENTION

In one aspect, the invention relates to a method for producing analcohol which comprises contacting a granular starch substrate with anacid-stable alpha amylase (asAA) having granular starch hydrolyzing(GSH) activity and a glucoamylase (GA) in a fermentation step whichfurther comprises ethanologenic microorganisms and producing an alcoholin the fermentation step. In some embodiments, the granular starchsubstrate is obtained from corn or wheat. In other embodiments, the asAAhaving GSH activity is obtained from the expression of a heterologouspolynucleotide in a fungal host cell which encodes an asAA having atleast 85%, 90% or 95% sequence identity to the sequence of SEQ ID NO: 3.In one preferred embodiment, the fermentation step includes the fungalcells which express the asAA and in other embodiments the fermentationstep includes a cell free asAA extract. In further embodiments, thefungal host cell is a Trichoderma cell. In other embodiments thealcohol, which is produced by the method is ethanol and theethanologenic microorganism is a yeast. In additional embodiments, theGA is produced from the expression of a heterologous polynucleotide in afungal host. In yet other embodiments, the alcohol is recovered from thefermentation.

In a second aspect, the invention relates to a fungal host cellcomprising a heterologous polynucleotide that encodes an acid-stablealpha amylase (asAA) having granular starch hydrolyzing (GSH) activitywhich has at least 85% or at least 90% sequence identity to the sequenceof SEQ ID NO: 3, and in some embodiments the heterologous polynucleotidewill encode an asAA having GSH activity with at least 95% sequenceidentity to the sequence of SEQ ID NO: 3. In some embodiments, the asAAhaving GSH activity, which is expressed from the fungal host, has alower pH optimum than an asAA having GSH activity obtained from a nativehost. In one embodiment, the fungal host cell is a Trichoderma cell. Ina further embodiment, the Trichoderma host cell is a T. reesei cell. Inanother embodiment, the fungal host cell is an Aspergillus cell.

In a third aspect, the invention relates to a granular starchhydrolyzing enzyme composition which comprises an acid-stable alphaamylase (asAA) having granular starch hydrolyzing (GSH) activity,wherein the asAA having GSH activity has at least 85%, 90% or 95%sequence identity to the sequence of SEQ ID NO: 3. In some embodiments,the enzyme composition comprises a truncated asAA having GSH activity,said enzyme having at least 970% sequence identity with SEQ ID NO: 9. Insome embodiments, the asAA will be obtained from the expression of aheterologous polynucleotide in a fungal host cell. In furtherembodiments, the fungal host cell will be a Trichoderma or Aspergillushost cell. In other embodiments, the composition will further include aglucoamylase enzyme. In some preferred embodiments, the glucoamylaseenzyme will be obtained from a strain of Aspergillus or Rhizopus. Inother embodiments, the glucoamylase will be a glucoamylase having GSHactivity and will be obtained from a strain of Aspergillus, Trichoderma,Rhizopus or Humicola. In other embodiments, both the asAA and theglucoamylase will be expressed in a fungal host having a heterologouspolynucleotide which expresses an asAA having GSH activity and aglucoamylase. In some embodiments, the fungal host strain will be thesame and in other embodiments, the fungal host strain will be different.In other embodiments, the invention relates to a method of hydrolyzinggranular starch using the enzyme composition of this aspect.

In a fourth aspect, the invention relates to a method of increasing thegranular starch hydrolyzing activity of a composition comprising aglucoamylase, which comprises adding an acid-stable alpha amylase (asAA)having granular starch hydrolyzing (GSH) activity to a composition whichincludes a granular starch substrate and a glucoamylase to produce asoluble starch hydrolysate. In some embodiments the asAA having GSHactivity has an amino acid sequence of at least 90% sequence identity toSEQ ID NO: 3 and in other embodiments, the asAA having GSH activity is atruncated asAA. In some embodiments, the truncated asAA includes asequence having at least 97% sequence identity with SEQ ID NO: 9. Infurther embodiments, the amount of solubilized starch is greater than acorresponding composition absent the asAA having GSH activity.

In a fifth aspect, the invention relates to a one-step method forproducing an alcohol, preferably ethanol, from a grain substratecomprising mixing in a fermentation medium under suitable fermentationconditions (i) a granular starch substrate derived from a grain, (ii) anacid-stable alpha amylase (asAA) having granular starch hydrolyzingactivity, and (iii) ethanologenic microorganisms to obtain a fermentedcomposition including an alcohol. In one embodiment, the asAA having GSHactivity has at least 90% sequence identity to the sequence of SEQ IDNO: 3. In another embodiment, the asAA having GSH activity is obtainedfrom expression in a Trichoderma host. In another embodiment, the asAAhaving GSH activity is a truncated asAA. In a further embodiment,glucoamylase is added to the step. In yet another embodiment, theinvention relates to the fermented composition obtained according tothis method. In another embodiment, the ethanol produced according tothe method encompassed by the invention is recovered. In otherembodiments, the grain is obtained from corn, wheat, barely, rye,potatoes, rice, sorghum or tapioca.

In a sixth aspect, the invention relates to a method for reducing theamount of residual starch in distillers' dried grains plus solids (DDGS)comprising producing an alcohol by a method of the invention, distillingthe alcohol to obtain a fermentation residue, and treating thefermentation residue to obtain distiller's dried grain with solubles. Insome embodiments, the amount of residual starch will be less than 20%and also less than 15%.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-B provide the genomic DNA sequence coding for the nativeAspergillus kawachi acid-stable alpha-amylase, which is designated asaA(SEQ ID NO:1). The eight putative introns are underlined.

FIG. 2 provides the signal sequence (SEQ ID NO: 2) and mature amino acidsequence (SEQ ID NO: 3) (AsaA) for A. kawachi acid stable alpha-amylase(SEQ ID NO: 4). The putative signal sequence (amino acids 1-21) isunderlined and bold. The putative linker isTTTTTTAATSTSKATTSSSSSSAAATTSSSCTATSTT (SEQ ID NO: 8). The amino acidsupstream of the linker, which are not underlined comprise the catalyticdomain (SEQ ID NO: 9) and the amino acids downstream of the linkercomprise the starch binding domain (SBD) (SEQ ID NO: 10). The SBDincludes the last 102 amino acids of the polypeptide of FIG. 2.

FIGS. 3A-D provide the complete nucleotide sequence (SEQ ID NO: 5),10990 bp, of plasmid pTrex3g_Akalpha (FIG. 4).

FIG. 4 provides a map of pTrex3g_Akalpha, which was used for expressionof the nucleic acid encoding the AsaA (Aspergillus kawachi asAA) andwhich contains EcoRI sites flanking the fungal expression vector,wherein

-   -   a) cbhI promoter is the Trichoderma reesei cellobiohydrolase        promoter;    -   b) asaA is the Aspergillus kawachi polynucleotide encoding the        acid stable alpha amylase of SEQ ID NO. 4;    -   c) cbhI terminator is the Trichoderma reesei cellobiohydrolase        terminator;    -   d) amdS is an Aspergillus nidulans acetamidase nutritional        marker gene; and    -   e) attB is a Gateway cloning system (Invitrogen) lambda phage        site for recombination.

FIGS. 5A and B provide an SDS-PAGE gel indicating the expression of asaAfrom Trichoderma reesei in a representative fermentation run forTrichoderma reesei clones as described in Example 5. In FIG. 5A, lane 1represents the standard See Blue+2 marker; lane 2 represents T. reeseiexpressed AsaA after 80 hours; lane 3 represents T. reesei expressedAsaA after 162 hours and lane 4 represents a T. reesei host cell controlat 162 hours in which the host cell has not been transformed with theasaA. An AsaA protein band is clearly observed at about 90 kDa and thisband is absent in the host strain control. In FIG. 5B, lane 1 representsT. reesei expressed AsaA after 210 hrs, lane 2 represents 3 bands of T.reesei expressed AsaA in intact and truncated form after 200 hours andlane 3 represents a molecular weight marker.

FIG. 6 illustrates the pH stability as % residual activity for thenative Aspergillus kawachi (nAk-AsaA) and the expressed A. kawachi(rAk-AsaA) in the T. reesei host (SEQ ID NO:3), as described in Example6.

FIG. 7 illustrates the % (v/v) ethanol (EtOH) production from thefermentation of corn flour mash at pH 5.0 with glucoamylase (0.5 GAU/gDISTILLASE) and an alpha amylase over time, wherein Tr-AsaA (A. kawachiacid stable alpha amylase expressed in Trichoderma reesei) isrepresented by AkM; SPEZYME LT75 alpha amylase is represented by LT75;SPEZYME FRED is represented by FRED; SPEZYME ETHYL is represented byETHYL; CLARASE is represented by FA and DISTILLASE is the control.Reference is made to Example 8.

FIG. 8 illustrates the degradation of granular starch as glucosereleased after 4 hours with incubated purified DISTILLASE (GA), purifiedAkM (A. kawachi acid stable alpha amylase expressed in Trichodermareesei), and the combination of AkAA and GA at pH 5.0. Reference is madeto Example 11.

FIG. 9 illustrates SEMs of granular corn starch incubated with theenzymes described for FIG. 8: purified DISTILLASE (GA), purified AkM (A.kawachi acid stable alpha amylase expressed in Trichoderma reesei), andthe combination of AkAA and GA.

FIG. 10A summarizes the final ethanol level as % (v/v) at different cornflour solids (% ds) as measured at 72 hours in fermentation.

FIG. 10B illustrates the % increase in ethanol with AkAA for each cornmash solids (% ds) plotted against mash solids (% ds).

FIG. 11 illustrates the % residual starch produced from different cornflour solids in fermentation with 0.5 GAU/g and AkAA (0.0 SSU/g or 1.5SSU/g) after 72 hours as further explained in example 12.

FIG. 12 depicts the % v/v ethanol measured at 71 hours for fermentationbroths comprising varying ratios of intact and truncated AkAA at fixeddosage level of 1.5 SSU/g ds AkAA.

FIG. 13 illustrates the amino acid sequence (SEQ ID NO: 11) of aglucoamylase derived from a strain of Trichoderma reesei.

FIG. 14 illustrates the amino acid sequence (SEQ ID NO: 12) of aglucoamylase derived from a strain of Humicola grisea var. thermoidea.

FIG. 15 illustrates the amino acid sequence (SEQ ID NO: 13) of aglucoamylase derived from a strain of Aspergillus kawachi.

FIG. 16 is a schematic diagram, which illustrates an embodiment of theinvention. This embodiment comprises combining a granular starchsubstrate with glucoamylase, asAA and microorganisms in a reactor toallow fermentation in a single step under conditions that includefermentation for 2 to 100 hours at a temperature of 25-40° C. Themixture that is produced in the fermentation is separated. Alcohol maybe recovered from the separation, and ethanol may be produced. Inaddition, a mixture of non-fermented solids and water may be recovered.The mixture of non-fermented solids and water, which includes residualstarch, stillage, proteins, and microorganisms, may be further processedto yield products such as DDG and DDGS or the components of the mixture(individually or combined) may be recycled back to the reactor forfurther fermentation.

DETAILED DESCRIPTION OF THE INVENTION

In some aspects, the present invention relies on routine techniques andmethods used in the field of genetic engineering and molecular biology.The following resources include descriptions of general methodologyuseful in accordance with the invention: Sambrook et al., MOLECULARCLONING: A LABORATORY MANUAL (2nd Ed., 1989); Kreigler, GENE TRANSFERAND EXPRESSION; A LABORATORY MANUAL (1990) and Ausubel et al., Eds.CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (1994). These general referencesprovide definitions and methods known to those in the art. However, itis not intended that the present invention be limited to any particularmethods, protocols, and reagents described, as these may vary.

Unless defined otherwise herein, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Singleton, et al.,DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley andSons, New York (1994) and Hale & Markham, THE HARPER COLLINS DICTIONARYOF BIOLOGY, Harper Perennial, NY (1991) provide one of skill withgeneral dictionaries of many of the terms used in this invention.

Although any methods and materials similar or equivalent to thosedescribed herein can be used in the practice or testing of the presentinvention, the preferred methods and materials are described.

The invention will now be described in detail by way of reference onlyusing the following definitions and examples. All patents andpublications, including all sequences disclosed within such patents andpublications, referred to herein are expressly incorporated byreference.

Numeric ranges are inclusive of the numbers defining the range.

Unless otherwise indicated, nucleic acids are written left to right in5′ to 3′ orientation; amino acid sequences are written left to right inamino to carboxy orientation, respectively.

The headings provided herein are not limitations of the various aspectsor embodiments of the invention which can be had by reference to thespecification as a whole.

A. DEFINITIONS

As used herein the term “starch” refers to any material comprised of thecomplex polysaccharide carbohydrates of plants, comprised of amylose andamylopectin with the formula (C₆H₁₀O₅)_(x), wherein X can be any number.In particular, the term refers to any plant-based material including butnot limited to grains, grasses, tubers and roots and more specificallywheat, barley, corn, rye, rice, sorghum, brans, cassava, millet, potato,sweet potato, and tapioca.

The term “granular starch” refers to raw (uncooked) starch, e.g.,granular starch that has not been subject to gelatinization.

The terms “granular starch hydrolyzing (GSH) enzyme” or “having granularstarch hydrolyzing (GSH) activity” refer to enzymes, which have theability to hydrolyze starch in granular form.

The term “alpha-amylase (e.g., E.C. class 3.2.1.1)” refers to enzymesthat catalyze the hydrolysis of alpha-1,4-glucosidic linkages. Theseenzymes have also been described as those effecting the exo orendohydrolysis of 1,4-α-D-glucosidic linkages in polysaccharidescontaining 1,4-α-linked D-glucose units. Another term used to describethese enzymes is “glycogenase”. Exemplary enzymes includealpha-1,4-glucan 4-glucanohydrase glucanohydrolase.

The term “acid-stable alpha amylase (“asAA”) refers to an alpha amylasethat is active in the pH range of pH 3.0 to 7.0 and preferably 3.5 to6.0.

The term “truncated asAA” refers to an asAA polypeptide having GSHactivity wherein at least a part of the SBD has been eliminated. In oneembodiment, a truncated asAA refers to an amino acid sequence whichincludes at least 65% of SEQ ID NO: 3. In a further embodiment, atruncated asAA will include at least 65% of an amino acid having atleast 90% sequence identity to SEQ ID NO: 3.

The term “starch binding domain (SBD)” refers to an amino acid sequencethat binds preferentially to a starch (polysaccharide) substrate.

The term “linker” refers to a short amino acid sequence generally havingbetween 3 to 40 amino acids, which covalently binds an amino acidsequence comprising a starch binding domain with an amino acid sequencecomprising a catalytic domain.

The term “catalytic domain” refers to a structural region of apolypeptide which is distinct from the SBD and which contains the activesite for substrate hydrolysis.

The term “glucoamylase” refers to the amyloglucosidase class of enzymes(e.g., EC.3.2.1.3, glucoamylase, 1,4-alpha-D-glucan glucohydrolase).These are exo-acting enzymes, which release glucosyl residues from thenon-reducing ends of amylose and amylopectin molecules. The enzyme alsohydrolyzes alpha-1,6 and alpha-1,3 linkages although at much slower ratethan alpha-1,4 linkages.

The term “glycosylation” refers to the post-transcriptional modificationof a protein by the addition of carbohydrate moieties, wherein thecarbohydrate is either N-linked or O-linked resulting in a glucoprotein.An N-linked carbohydrate moiety of a glycoprotein is attached by aglycosidic bond to the β-amide nitrogen of an asparagine residue. AnO-linked carbohydrate is attached by a glycosidic bond to a proteinthrough the hydroxy group of a serine or a threonine residue.

The term “recombinant” when used in reference to a cell, nucleic acid,protein or vector, indicates that the cell, nucleic acid, protein orvector, has been modified by the introduction of a heterologous nucleicacid or protein or the alteration of a native nucleic acid or protein,or that the cell is derived from a cell so modified. Thus, for example,recombinant cells express genes that are not found within the native(non-recombinant) form of the cell or express native genes that areotherwise abnormally expressed, under expressed or not expressed at all.

The terms “protein” and “polypeptide” are used interchangeably herein.The conventional one-letter or three-letter code for amino acid residuesis used herein.

A “signal sequence” means a sequence of amino acids bound to theN-terminal portion of a protein, which facilitates the secretion of themature form of the protein outside the cell. The definition of a signalsequence is a functional one. The mature form of the extracellularprotein lacks the signal sequence which is cleaved off during thesecretion process.

The term “native acid-stable alpha amylase (n-asAA)” refers to an asAAproduced from the endogenous expression of the asAA. For example, theterm “n-asaA” means the endogenous expression of an acid-stable alphaamylase (ie, SEQ ID NO: 3) from an Aspergillus kawachi.

The terms “recombinant acid-stable alpha amylase (r-asAA)”,“recombinantly expressed asAA” and “recombinantly produced asAA” referto a mature asAA protein sequence that is produced in a host cell fromthe expression of a heterologous polynucleotide. For example, the term“r-asaA” means the Aspergillus kawachi acid-stable alpha amylase (i.e.,SEQ ID NO: 3) is expressed and produced in a host in which apolynucleotide encoding the asaA has been introduced. The mature proteinsequence of a r-asAA excludes a signal sequence.

A “gene” refers to a DNA segment that is involved in producing apolypeptide and includes regions preceding and following the codingregions as well as intervening sequences (introns) between individualcoding segments (exons).

The term “nucleic acid” encompasses DNA, RNA, single stranded or doublestranded and chemical modifications thereof. The terms “nucleic acid”and “polynucleotide” may be used interchangeably herein. Because thegenetic code is degenerate, more than one codon may be used to encode aparticular amino acid, and the present invention encompassespolynucleotides, which encode a particular amino acid sequence.

A “vector” refers to a polynucleotide sequence designed to introducenucleic acids into one or more cell types. Vectors include cloningvectors, expression vectors, shuttle vectors, plasmids, phage particles,cassettes and the like.

An “expression vector” as used herein means a DNA construct comprising aDNA sequence which is operably linked to a suitable control sequencecapable of effecting expression of the DNA in a suitable host. Suchcontrol sequences may include a promoter to effect transcription, anoptional operator sequence to control transcription, a sequence encodingsuitable ribosome binding sites on the mRNA, enhancers and sequenceswhich control termination of transcription and translation.

A “promoter” is a regulatory sequence that is involved in binding RNApolymerase to initiate transcription of a gene. The promoter may be aninducible promoter or a constitutive promoter. A preferred promoter usedin the invention is Trichoderma reesei cbh1, which is an induciblepromoter.

“Under transcriptional control” is a term well understood din the artthat indicates that transcription of a polynucleotide sequence, usuallya DNA sequence, depends on its being operably linked to an element whichcontributes to the initiation of, or promotes transcription.

“Under translational control” is a term well understood in the art thatindicates a regulatory process that occurs after mRNA has been formed.

As used herein when describing proteins and genes that encode them, theterm for the gene is italicized, (e.g., the gene that encodes asaA (A.kawachi asAA) may be denoted as asaA). The term for the protein isgenerally not italicized and the first letter is generally capitalized,(e.g., the protein encoded by the asaA gene may be denoted as AsaA orasaA).

The term “derived” encompasses the terms “originated from”, “obtained”or “obtainable from”, and “isolated from” and as used herein means thata polypeptide encoded by the nucleotide sequence is produced from a cellin which the nucleotide is naturally present or in which the nucleotidehas been inserted.

The term “operably linked” refers to juxtaposition wherein the elementsare in an arrangement allowing them to be functionally related. Forexample, a promoter is operably linked to a coding sequence if itcontrols the transcription of the sequence.

The term “selective marker” refers to a gene capable of expression in ahost that allows for ease of selection of those hosts containing anintroduced nucleic acid or vector. Examples of selectable markersinclude but are not limited to antimicrobials (e.g., hygromycin,bleomycin, or chloramphenicol) and/or genes that confer a metabolicadvantage, such as a nutritional advantage on the host cell.

A polynucleotide or a polypeptide having a certain percent (e.g. 80%,85%, 90%, 95%, or 99%) of sequence identity with another sequence meansthat, when aligned, that percentage of bases or amino acid residues arethe same in comparing the two sequences. This alignment and the percenthomology or identity can be determined using any suitable softwareprogram known in the art, for example those described in CURRENTPROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel et al. (eds) 1987,Supplement 30, section 7.7.18). Preferred programs include the GCGPileup program, FASTA (Pearson et al. (1988) Proc. Natl, Acad. Sci. USA85:2444-2448), and BLAST (BLAST Manual, Altschul et al., Natl. Cent.Biotechnol. Inf., Natl Lib. Med. (NCIB NLM NIH), Bethesda, Md., andAltschul et al., (1997) NAR 25:3389-3402). Another preferred alignmentprogram is ALIGN Plus (Scientific and Educational Software, PA),preferably using default parameters. Another sequence software programthat finds use is the TFASTA Data Searching Program available in theSequence Software Package Version 6.0 (Genetics Computer Group,University of Wisconsin, Madison, Wis.).

One skilled in the art will recognize that sequences encompassed by theinvention are also defined by the ability to hybridize under stringenthybridization conditions with the exemplified asaA sequence (e.g., SEQID NO:1). A nucleic acid is hybridizable to another nucleic acidsequence when a single stranded form of the nucleic acid can anneal tothe other nucleic acid under appropriate conditions of temperature andsolution ionic strength. Hybridization and washing conditions are wellknown in the art (See, e.g., Sambrook (1989) supra, particularlychapters 9 and 11). In some embodiments, stringent conditions correspondto a Tm of 65° C. and 0.1×SSC, 0.1% SDS.

“Host strain” or “host cell” means a suitable host for an expressionvector or DNA construct comprising a polynucleotide encoding a granularstarch hydrolyzing enzyme according to the invention. Specifically, hoststrains are preferably filamentous fungal cells. The host cell may be awild type filamentous fungal host cell or a genetically modified hostcell. In a preferred embodiment of the invention, “host cell” means boththe cells and protoplasts created from the cells of a filamentous fungalstrain and particularly a Trichoderma sp. or an Aspergillus sp.

The term “filamentous fungi” refers to all filamentous forms of thesubdivision Eumycotina (See, Alexopoulos, C. J. (1962), INTRODUCTORYMYCOLOGY, Wiley, New York and AINSWORTH AND BISBY DICTIONARY OF THEFUNGI, 9^(th) Ed (2001), Kirk et al Eds., CAB, InternationalPublishing). These fungi are characterized by a vegetative mycelium witha cell wall composed of chitin, cellulose, and other complexpolysaccharides. The filamentous fungi of the present invention aremorphologically, physiologically, and genetically distinct from yeasts.Vegetative growth by filamentous fungi is by hyphal elongation andcarbon catabolism is obligatory aerobic. In the present invention, thefilamentous fungal parent cell may be a cell of a species of, but notlimited to, Trichoderma, (e.g., Trichoderma reesei (previouslyclassified as T. longibrachiatum and currently also known as Hypocreajecorina), Trichoderma viride, Trichoderma koningii, Trichodermaharzianum); Penicillium sp., Humicola sp. (e.g., Humicola insolens andHumicola grisea); Chrysosporium sp. (e.g., C. lucknowense), Gliocladiumsp., Aspergillus sp. (e.g., A. oryzae, A. kawachi, A. niger, and A.awamori), Fusarium sp., Neurospora sp., Hypocrea sp., and Emericella sp.(See also, Innis et al., (1985) Sci. 228:21-26).

As used herein, the term “Trichoderma” or “Trichoderma sp.” refer to anyfungal genus previously or currently classified as Trichoderma.

The term “culturing” refers to growing a population of microbial cellsunder suitable conditions in a liquid or solid medium. In oneembodiment, culturing refers to fermentative bioconversion of a starchsubstrate containing granular starch to an end-product (typically in avessel or reactor). Fermentation is the enzymatic and anaerobicbreakdown of organic substances by microorganisms to produce simplerorganic compounds. While fermentation occurs under anaerobic conditionsit is not intended that the term be solely limited to strict anaerobicconditions, as fermentation also occurs in the presence of oxygen.

The phrase “simultaneous saccharification and fermentation (SSF)” refersto a process in the production of end products in which a microbialorganism, such as an ethanol producing microorganism and at least oneenzyme such as an asAA are in the same process step. In one embodimentof the present invention, SSF refers to the contemporaneous hydrolysisof granular starch substrates to saccharides including glucose and thefermentation of the saccharides into alcohol in the same reactor vessel.

The term “contacting” refers to the placing of the respective enzyme(s)in sufficiently close proximity to the respective substrate to enablethe enzyme(s) to convert the substrate to the end-product. Those skilledin the art will recognize that mixing solutions of the enzyme with therespective substrates can effect contacting.

The term “enzymatic conversion” in general refers to the modification ofa substrate by enzyme action. The term as used herein also refers to themodification of a is granular starch substrate by the action of anenzyme.

As used herein the term “saccharification” refers to enzymaticconversion of starch to glucose.

The term “gelatinization” means solubilization of a starch molecule bycooking to form a viscous suspension.

The term “gelatinization temperature” refers to the temperature at whichgelatinization of a starch begins. The exact temperature ofgelatinization depends on the specific starch and may vary depending onfactors such as, plant species and environmental and growth conditions.

The phrase “below the gelatinization temperature” refers to atemperature less than the temperature which starts gelatinization.

The term “liquefaction” refers to the stage in starch conversion inwhich gelatinized starch is hydrolyzed to give low molecular weightsoluble dextrins.

The term “degree of polymerization (DP)” refers to the number (n) ofanhydroglucopyranose units in a given saccharide. Examples of DP1 arethe monosaccharides, such as glucose and fructose. Examples of DP2 arethe disaccharides, such as maltose and sucrose. A DP>3 denotes polymerswith a degree of polymerization of greater than 3.

The terms “end-product” or “desired end-product” refer to anycarbon-source derived molecule product which is enzymatically convertedfrom the granular starch substrate.

As used herein the term “dry solids content (ds)” refers to the totalsolids of a slurry in % on a dry weight basis.

The term “slurry” refers to an aqueous mixture containing insolublesolids.

The term “residual starch” refers to the remaining starch (soluble orinsoluble) left in a composition after fermentation of a starchcontaining substrate.

The term “soluble starch hydrolysate” refers to soluble productsresulting from starch hydrolysis, which may comprise mono-, di-, oroligosaccharides (e.g. glucose, maltose and higher sugars).

As used herein “a recycling step” refers to the recycling of mashcomponents, which may include residual starch, enzymes and/ormicroorganisms to ferment substrates comprising granular starch.

The term “mash” refers to a mixture of a fermentable carbon source(carbohydrate) in water used to produce a fermented product, such as analcohol. In some embodiments, the term “beer”, “mash” and “fermentationbroth” may be used interchangeability.

The term “stillage” means a mixture of non-fermented solids and water,which is the residue after removal of alcohol from a fermented mash.

The terms “distillers dried grain (DDG)” and “distillers dried grainwith solubles (DDGS)” refer to useful co-products of grain fermentation.

As used herein “ethanologenic microorganism” refers to a microorganismwith the ability to convert a sugar or oligosaccharide to ethanol. Theethanologenic microorganisms are ethanologenic by virtue of theirability to express one or more enzymes that individually or togetherconvert sugar to ethanol.

As used herein the term “ethanol producer” or ethanol producingmicroorganism” refers to any organism or cell that is capable ofproducing ethanol from a hexose or pentose. Generally, ethanol-producingcells contain an alcohol dehydrogenase and a pyruvate decarboxylase.Examples of ethanol producing microorganisms include fungalmicroorganisms such as yeast. A preferred yeast includes strains ofSaccharomyces, particularly, S. cerevisiae.

The term “heterologous” with reference to a polynucleotide or proteinrefers to a polynucleotide or protein that does not naturally occur in ahost cell. In some embodiments, the protein is a commercially importantindustrial protein. It is intended that the term encompass proteins thatare encoded by naturally occurring genes, mutated genes, and/orsynthetic genes.

The term “endogenous” with reference to a polynucleotide or proteinrefers to a polynucleotide or protein that occurs naturally in the hostcell.

The terms “recovered”, “isolated”, and “separated” as used herein referto a compound, protein, cell, nucleic acid or amino acid that is removedfrom at least one component with which it is naturally associated.

As used herein, the terms “transformed”, “stably transformed” and“transgenic” used in reference to a cell means the cell has a non-native(e.g., heterologous) nucleic acid sequence integrated into its genome oras an episomal plasmid that is maintained through multiple generations.

As used herein, the term “expression” refers to the process. by which apolypeptide is produced based on the nucleic acid sequence of a gene.The process includes both transcription and translation.

The term “introduced” in the context of inserting a nucleic acidsequence into a cell, means “transfection”, or “transformation” or“transduction” and includes reference to is the incorporation of anucleic acid sequence into a eukaryotic or prokaryotic cell wherein thenucleic acid sequence may be incorporated into the genome of the cell(e.g., chromosome, plasmid, plastid, or mitochondrial DNA), convertedinto an autonomous replicon, or transiently expressed (e.g., transfectedmRNA).

As used herein the term “specific activity” means an enzyme unit definedas the number of moles of substrate converted to product by an enzymepreparation per unit time under specific conditions. Specific activityis expressed as units (U)/mg of protein.

As used herein the term “enzyme unit” refers to the amount of enzymethat produces a given amount of product per given amount of time underassay conditions. In some embodiments, an enzyme unit refers to theamount of enzyme that produces 1 micromole of product per minute underthe specified conditions of the assay. For example, in one embodiment,the term “glucoamylase activity unit” (GAU) is defined as the amount ofenzyme required to produce 1 g of glucose per hour from soluble starchsubstrate (4% ds) under assay conditions of 60° C. and pH 4.2.

In another embodiment, a granular starch hydrolyzing enzyme unit (GSHEU) is defined as being the amount of GSHE required to produce 1 mg ofglucose per minute from granular starch under assay conditions of, forexample 25° C. at pH 5.0. In a preferred embodiment, a GSHE U is definedas being the amount of a GSHE required to produce 1 mg glucose/min froma granular starch substrate at 50° C. at pH 4.5.

The term “yield” refers to the amount of end-product or desiredend-products produced using the methods of the present invention. Insome preferred embodiments, the yield is greater than that producedusing methods known in the art. In some embodiments, the term refers tothe volume of the end product and in other embodiment the term refers tothe concentration of the end product.

“ATCC” refers to American Type Culture Collection located at Manassas,Va. 20108 (ATCC; <www.atcc.org>).

“NRRL” refers to the Agricultural Research Service Culture Collection,National Center for Agricultural Utilization Research (and previouslyknown as USDA Northern Regional Research Laboratory), Peoria, Ill.

“A”, “an” and “the” include plural references unless the context clearlydictates otherwise.

As used herein the term “comprising” and its cognates are used in theirinclusive sense; that is, equivalent to the term “including” and itscorresponding cognates.

B. PREFERRED EMBODIMENTS

The present invention relates to a granular starch hydrolyzing enzymecomposition which comprises an acid-stable alpha amylase (asAA) havinggranular starch hydrolyzing (GSH) activity and optionally comprising aglucoamylase, wherein the asAA has at least 85%, 90% and 95% sequenceidentity to the sequence of SEQ ID NO: 3. In certain preferredembodiments, the invention provides means for the production of desiredend-products of the bioconversion of a granular starch substrate and inpreferred embodiments, the asAA is contacted with a slurry of a granularstarch substrate and the granular starch substrate is directly convertedto an end-product without gelatinization and liquefaction of thegranular starch substrate.

Granular Starch Substrates—

A granular starch substrate to be processed in the methods of theinvention may be obtained from any plant part including stems, grains,roots and tubers. Particularly preferred plant sources include corn;wheat; rye; sorghum; rice; millet; barley; cassava; legumes, such asbeans and peas; sugarcane; potatoes; sweet potatoes; bananas; andtapioca.

Specifically contemplated starch substrates are cornstarch and wheatstarch. The starch from a grain may be ground or whole and includes cornsolids, such as kernels, bran and/or cobs. In addition the grain may befractionated (e.g., endosperm, germ or fiber (bran) for corn and gluten,starch A or B for wheat). The starch may be highly refined raw starch orfeedstock from starch refinery processes. Those of general skill in theart are well aware of available methods which may be used to preparegranular starch substrates for use in the methods encompassed by theinvention. Some of these methods include dry milling of whole cerealgrains using hammer mills and roller mills and wet milling.

In some embodiments, at least 80%, 70%, 60%, 50%, 40% 30% of the milledcereal grain will pass through a 0.5 mm screen. In other embodiments, afiner particle size is preferred, and therefore at least 80%, 85%, 90%and 95% of the milled cereal grain will pass through a 0.5 mm screen. Inyet other embodiments, the milled cereal grain may be a coarse particleand in these instances at least 90% of the milled grain will passthrough a 1.0 mm, a 1.5 mm or a 2.0 mm screen but only about less than5%, 10% and 15% will pass through a 0.5 mm screen.

Various starches are commercially available. For example, cornstarchesare available from Cerestar, Sigma, and Katayama Chemical Industry Co.(Japan); wheat starches are available from Sigma; sweet potato starchesare available from Wako Pure Chemical Industry Co. (Japan); and potatostarch is available from Nakaari Chemical Pharmaceutical Co. (Japan).

Various references have reported on the amount of starch found in cerealgrains and reference is made to The Alcohol Textbook, 3^(rd) Ed. K.Jacques et al., Eds. 1999, Nottingham University Press. For example corncontains about 60-68% starch; barley contains about 55-65% starch;millet contains about 75-80% starch; wheat contains about 60-65% starch;and polished rice contains 70-72% starch.

In some embodiments of the method encompassed by the invention, thegranular starch substrate is slurried (generally with water) and theslurry comprises i) about 10 to about 55% dry solids content (ds); ii)about 15 to about 50% dry solids content; iii) about 20 to about 45% drysolids content; iv) about 25 to about 45% dry solids content; v) about30 to about 45% dry solids content; vi) about 30 to about 40% dry solidscontent; and also vii) about 30 to 35% dry solids content.

Acid-Stable Alpha Amylases (asAA) Having Granular Starch Hydrolyzing(GSH) Activity—

In one embodiment, an asAA having GSH activity is obtained from a strainof Aspergillus, e.g., A. oryzae, A. kawachi, A. niger, and A. awamori.In a preferred embodiment, the asAA having GSH activity is obtained froma strain of Aspergillus kawachi.

In a particularly preferred embodiment, the asAA having GSH activitycomprises an amino acid sequence having at least 80%, at least 85%, atleast 90%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98% and at least 99% sequence identity with theamino acid sequence set forth in SEQ ID NO: 3. In another embodiment,the asAA having GSH activity comprises an amino acid sequence having atleast 90% sequence identity with SEQ ID NO: 3. In a further embodiment,the asAA having GSH activity comprises an amino acid sequence having atleast 95% sequence identity to SEQ ID NO: 3. The asAA may also comprisean amino acid sequence having at least 98% sequence identity with SEQ IDNO: 3. In a further embodiment, the asAA having GSH activity comprisesthe amino acid sequence of SEQ ID NO: 3. In some embodiments, SE ID NO:3 or a sequence having at least 85% sequence identity thereto isconsidered an intact asAA.

In some embodiments, the asAA having GSH activity will include acatalytic domain having at least 96%, 97%, 98% and 99% sequence identitywith SEQ ID NO: 9. In other embodiments, the asAA having GSH activitywill include a SBD having at least 70%, 75%, 80%, 85%, 90%, 93%, 95%,96%, 97% 98% and 99% sequence identity with the SBD of SEQ ID NO: 10.

In further embodiments, the asAA having GSH activity will comprise atleast 97%, 98%, and 99% sequence identity with SEQ ID NO: 9; at least96%, 97%, 98% and 99% sequence identity with SEQ ID NO: 8; and at least95%, 96%, 97%, 98% and 99% sequence identity with SEQ ID NO: 10. Inpreferred embodiments, the catalytic domain and the SBD are obtainedfrom an alpha amylase of an Aspergillus kawachi strain.

In other embodiments, the asAA having GSH activity is a truncatedenzyme. In some embodiments, the truncated asAA having GSH activity willinclude at least 60%, 65%, 70%, 75%, 80%, 83%, 85%, 88%, 90%, 93%, 95%,96%, 97%, 98% and 99% of the amino acid sequence of SEQ ID NO: 3 or anamino acid sequence having at least 90% and preferably 95% sequenceidentity with SEQ ID NO: 3. The enzyme may be truncated at the carboxyterminus end of the polypeptide.

In some embodiments, the truncated asAA having GSH activity will includeat least 90%, 95%, 96%, 97%, 98% and 99% of the catalytic domain of SEQID NO: 9 or a sequence having at least 97%, 98% and 99% sequenceidentity thereto.

In other embodiments, the truncated asAA will include at least 430, atleast 440, at least 450, at least 460 and at least 470 amino acids ofSEQ ID NO: 3 or a sequence having GSH activity and at least 90% sequenceidentity to SEQ ID NO: 3.

In some embodiments, the truncated asAA having GSH activity will includethe catalytic domain of SEQ ID NO: 9 or a sequence having at least 96%,97%, 98% and 99% sequence identity thereto and a linker having at least90%, 95%, 96%, 97%, 98% and 99% sequence identity to SEQ ID NO: 8.Preferably the truncated enzyme will include a catalytic domain havingat least 97% sequence identity with SEQ ID NO: 9 and a linker having atleast 95% sequence identity with SEQ ID NO: 8. In some embodiments, thetruncated enzyme will include a catalytic domain having at least 96%,97%, 98% and 99% sequence identity to SEQ ID NO: 9 and at least about 5,10, 20, 25, 30 and 35 amino acids located downstream of the catalyticdomain. In other embodiments, the truncated enzyme will include acatalytic domain and a linker as defined above and further a portion ofthe SBD having at least 70%, 75%, 80%, 85%, 90%, 93%, 95%, 96%, 97%, 98%and 99% sequence identity to the sequence of SEQ ID NO: 10. The portionof the SBD will include at least about 5, 10, 20, 30, 40, 50, 60, 70,80, 90, and 100 amino acids located downstream of the linker.

In other embodiments, the asAA comprising the amino acid sequence of SEQID NO: 3 or an amino acid sequence having at least 95% sequence identitywith SEQ ID NO: 3 is encoded by a polynucleotide having at least 70%, atleast 80%, at least 85%, at least 90%, at least 93%, at least 95%, atleast 96%, at least 97%, at least 98% and at least 99% sequence identityto the sequence of SEQ ID NO: 1. In a particularly preferred embodiment,the nucleic acid sequence encoding the asAA of SEQ ID NO: 3 (AsaA) isthe nucleic acid sequence of SEQ ID NO: 1.

Recombinantly Expressed Enzymes and Host Cells—

In some embodiments of the invention, microorganisms are geneticallyengineered to express heterologous asAA having GSH activity andmicroorganisms may also be engineered to express heterologousglucoamylases. Preferred host cells are filamentous fungal cells. In apreferred embodiment, the filamentous fungal host is a strain of anAspergillus sp, a Trichoderma sp, a Fusarium sp and a Penicillium sp.Particularly preferred fungal host cells include A. nidulans, A.awamori, A. oryzae, A. aculeatus, A. niger, A. japonicus, T. reesei, T.viride, F. oxysporum, and F. solani. Aspergillus strains are disclosedin Ward et al. (1993) Appl. Microbiol. Biotechnol. 39:738-743 andGoedegebuur et al., (2002) Curr Gene 41:89-98. In a most preferredembodiment, the host is a strain of Trichoderma, and particularly astrain of T. reesei. Strains of T. reesei are known and nonlimitingexamples include ATCC No. 13631, ATCC No. 26921, ATCC No. 56764, ATCCNo. 56765, ATCC No. 56767 and NRRL 15709. In some preferred embodiments,the host strain is a derivative of RL-P37. RL-P37 is disclosed inSheir-Neiss et al. (1984) Appl. Microbiol. Biotechnology 20:46-53.

In some preferred embodiments, a Trichoderma host cell or an Aspergillushost cell is genetically engineered to express an asAA having GSHactivity characterized by an amino acid sequence having at least 80%,85%, 90%, 95%, 96%, 97%, 98% and 99% identity with SEQ ID NO: 3. Infurther embodiments, the asAA having GSH activity will comprise at least97%, 98%, and 99% sequence identity with SEQ ID NO: 9; at least 96%,97%, 98% and 99% sequence identity with SEQ ID NO: 8; and at least 95%,96%, 97%, 98% and 99% sequence identity with SEQ ID NO: 10. In preferredembodiments, the asAA is obtained from an alpha amylase of anAspergillus kawachi strain.

In some embodiments, the invention comprises polynucleotides which codefor the asAA of SEQ ID NO: 3, the asAA of SEQ ID NO: 9 or a truncatedenzyme as defined herein. In addition, the polynucleotide may code foran AsAA having GSH activity which comprises an amino acid having atleast 95%, 98% and 99% identity with the sequence of SEQ ID NO: 3 or atleast 97%, 98% and 99% identity with the sequence of SEQ ID NO: 9. Insome embodiments, the polynucleotide encoding an asAA will have anucleic acid sequence of SEQ ID NO: 1 or a nucleic acid sequence havingat least 70% sequence identity with SEQ ID NO: 1.

In some embodiments, the asAA produced in a host cell engineered toinclude a heterologous polynucleotide encoding an asAA having GSHactivity will have different, such as improved properties compared tothe asAA produced by the endogenous expression of the asAA having GSHactivity in a native host. These properties may include for example,increased enzyme activity, increased enzyme stability at lower pH levelsor increased specific activity. In some embodiments, a heterologouslyproduced asAA having GSH activity according to the invention willexhibit a maximum pH activity within a pH range of 3.0 to 6.0; a pHrange of 3.0 to 5.0; a pH range of 3.5 to 5.0 and also within a pH rangeof 3.5 to 4.5. In other embodiments, a heterologously produced asAA willhave a greater stability or residual activity at a pH level of 3.0, 3.5,4.0, 4.5 and/or 5.0 compared to a corresponding asAA endogenouslyproduced from a native host under essentially the same conditions. Insome embodiments the level of enzyme stability for a heterologouslyproduced asAA will be at least 0.5, at least 1.0, at least 2.0 or atleast 2.5 times greater at a specific pH level compared to anendogenously expressed asAA at the same pH level. In some embodiments,these improved or different properties of the heterologously expressedasAA having GSH activity are particularly apparent in Trichoderma hostcells. In some embodiments, the heterologously expressed asAA will beproduced as an intact asAA having GSH activity which includes thecatalytic domain, linker and SBD, for example the mature polypeptideillustrated in FIG. 2 (SEQ ID NO: 3). In other embodiments, theheterologously expressed asAA will be produced as a truncated asAAhaving GSH activity, for example, wherein the SBD is partially orcompletely cleaved off the catalytic domain.

In other embodiments, the host strain which is genetically engineered toexpress an asAA having GSH activity may also be genetically engineeredto express a heterologous GA.

A host strain useful in the invention may have been previouslymanipulated through genetic engineering. In some embodiments, thegenetically engineered host cell or strain may be a protease deficientstrain. In other embodiments, expression of various native genes of thefungal host cell will have been reduced or inactivated. These genesinclude, for example genes encoding proteases and cellulolytic enzymes,such as endoglucanases (EG) and exocellobiohydrolases (CBH) (e.g. cbh1,cbh2, egl1, egl2 and egl3). U.S. Pat. No. 5,650,322 discloses derivativestrains of RL-P37 having deletions in the cbh1 gene and the cbh2 gene.Also reference is made to U.S. Pat. No. 5,472,864.

Vectors—While the description below refers specifically to asAA, oneskilled in the art will readily understand that the same or similarmethods apply to DNA constructs and vectors useful for introduction of apolynucleotide encoding GA into a host cell.

According to the invention, a DNA construct comprising nucleic acidencoding an asAA encompassed by the invention is constructed to transferan asAA into a host cell. In one embodiment, the DNA construct istransferred to a host cell by an expression vector which comprisesregulatory sequences operably linked to an asAA coding sequence.

The vector may be any vector which when introduced into a fungal hostcell is integrated into the host cell genome and is replicated.Reference is made to the Fungal Genetics Stock Center Catalogue ofStrains (FGSC, <www.fgsc.net>) for a list of vectors. Additionalexamples of suitable expression and/or integration vectors are providedin Sambrook et al., (1989) supra, Ausubel (1987) supra, van den Hondelet al. (1991) in Bennett and Lasure (Eds.) MORE GENE MANIPULATIONS INFUNGI, Academic Press pp. 396-428 and U.S. Pat. No. 5,874,276.Particularly useful vectors include pFB6, pBR322, PUC18, pUC100 andpENTR/D.

In preferred embodiments, nucleic acid encoding an asAA encompassed bythe invention is operably linked to a suitable promoter, which showstranscriptional activity in the fungal host cell. The promoter may bederived from genes encoding proteins either homologous or heterologousto the host cell. Preferably, the promoter is useful in a Trichodermahost. Suitable nonlimiting examples of promoters include cbh1, cbh2,egl1, egl2, pepA, hfb1, hfb2, xyn1 and amy. In one embodiment, thepromoter is one that is native to the host cell. For example, when T.reesei is the host, the promoter is a native T. reesei promoter. In apreferred embodiment, the promoter is T. reesei cbh1, which is aninducible promoter and has been deposited in GenBank under Accession No.D86235. An “inducible promoter” is a promoter that is active underenvironmental or developmental regulation. In another embodiment, thepromoter is one that is heterologous to the fungal host cell. Otherexamples of useful promoters include promoters from the genes of A.awamori and A. niger glucoamylase (glaA) (Nunberg et al., (1984) Mol.Cell Biol. 4:2306-2315 and Boel et al., (1984) EMBO J. 3:1581-1585);Aspergillus niger alpha amylases, Aspergillus oryzae TAKA amylase, T.reesei xln1 and the T. reesei cellobiohydrolase 1 (EPA 137280A1).

In some preferred embodiments, the asAA coding sequence is operablylinked to a signal sequence. The DNA encoding the signal sequence ispreferably that which is naturally associated with the asAA gene to beexpressed. Preferably, the signal sequence is encoded by an Aspergilluskawachi asaA gene that encodes an Ak-asaA. More preferably the signalsequence has at least 90%, at least 95%, at least 97%, and at least 99%sequence identity to the signal sequence of SEQ ID NO: 2. In additionalembodiments, a signal sequence and a promoter sequence comprising a DNAconstruct or vector to be introduced into a fungal host cell are derivedfrom the same source. For example, in some embodiments, the signalsequence is the cdh1 signal sequence which is operably linked to a cdh1promoter.

In some embodiments, the expression vector also includes a terminationsequence. In one embodiment, the termination sequence and the promotersequence are derived from the same source. In another embodiment, thetermination sequence is homologous to the host cell. A particularlysuitable terminator sequence is cbh1 derived from a Trichoderma strainand particularly T. reesei. Other useful fungal terminators include theterminator from A. niger or A. awamori glucoamylase gene (Nunberg et al.(1984) supra, and Boel et al., (1984) supra).

In some embodiments, an expression vector includes a selectable marker.Examples of preferred selectable markers include ones which conferantimicrobial resistance (e.g., hygromycin and phleomycin). Nutritionalselective markers also find use in the present invention including thosemarkers known in the art as amdS argB and pyr4. Markers useful in vectorsystems for transformation of Trichoderma are known in the art (See,e.g., Finkelstein, chapter 6 in BIOTECHNOLOGY OF FILAMENTOUS FUNGI,Finkelstein et al. Eds. Butterworth-Heinemann, Boston, Mass. (1992),Chap. 6.; and Kinghorn et al. (1992) APPLIED MOLECULAR GENETICS OFFILAMENTOUS FUNGI, Blackie Academic and Professional, Chapman and Hall,London). In a preferred embodiment, the selective marker is the amdSgene, which encodes the enzyme acetamidase, allowing transformed cellsto grow on acetamide as a nitrogen source. The use of A. nidulans amdSgene as a selective marker is described in Kelley et al., (1985) EMBO J.4:475-479 and Penttila et al., (1987) Gene 61:155-164.

An expression vector comprising a DNA construct with a polynucleotideencoding an asAA may be any vector which is capable of replicatingautonomously in a given fungal host organism or of integrating into theDNA of the host. In some embodiments, the expression vector is aplasmid. In preferred embodiments, two types of expression vectors forobtaining expression of genes are contemplated.

The first expression vector comprises DNA sequences in which thepromoter, asAA coding region, and terminator all originate from the geneto be expressed. In some embodiments, gene truncation is obtained bydeleting undesired DNA sequences (e.g., DNA encoding unwanted domains)to leave the domain to be expressed under control of its owntranscriptional and translational regulatory sequences.

The second type of expression vector is preassembled and containssequences required for high-level transcription and a selectable marker.In some embodiments, the coding region for an asAA gene or part thereofis inserted into this general-purpose expression vector such that it isunder the transcriptional control of the expression construct promoterand terminator sequences. In some embodiments, genes or part thereof areinserted downstream of the strong cbh1 promoter.

Methods used to ligate the DNA construct comprising a polynucleotideencoding an asAA, a promoter, a terminator and other sequences and toinsert them into a suitable vector are well known in the art. Linking isgenerally accomplished by ligation at convenient restriction sites. Ifsuch sites do not exist, the synthetic oligonucleotide linkers are usedin accordance with conventional practice. (See, Sambrook (1989) supra,and Bennett and Lasure, MORE GENE MANIPULATIONS IN FUNGI, AcademicPress, San Diego (1991) pp 70-76.). Additionally, vectors can beconstructed using known recombination techniques (e.g., Invitrogen LifeTechnologies, Gateway Technology).

Where it is desired to obtain a fungal host cell having one or moreinactivated genes known methods may be used (e.g. methods disclosed inU.S. Pat. No. 5,246,853, U.S. Pat. No. 5,475,101 and WO92/06209). Geneinactivation may be accomplished by complete or partial deletion, byinsertional inactivation or by any other means which renders a genenonfunctional for its intended purpose (such that the gene is preventedfrom expression of a functional protein). Any gene from a Trichoderma spor other filamentous fungal host, which has been cloned can be deleted,for example cbh1, cbh2, egl1 and egl2 genes. In some embodiments, genedeletion may be accomplished by inserting a form of the desired gene tobe inactivated into a plasmid by methods known in the art. The deletionplasmid is then cut at an appropriate restriction enzyme site(s),internal to the desired gene coding region, and the gene coding sequenceor part thereof is replaced with a selectable marker. Flanking DNAsequences from the locus of the gene to be deleted (preferably betweenabout 0.5 to 2.0 kb) remain on either side of the marker gene. Anappropriate deletion plasmid will generally have unique restrictionenzyme sites present therein to enable the fragment containing thedeleted gene, including the flanking DNA sequences and the selectablemarkers gene to be removed as a single linear piece.

Transformation, Expression and Culture of Host Cells—

Introduction of a DNA construct or vector into a host cell includestechniques such as transformation; electroporation; nuclearmicroinjection; transduction; transfection, (e.g., lipofection mediatedand DEAE-Dextrin mediated transfection); incubation with calciumphosphate DNA precipitate; high velocity bombardment with DNA-coatedmicroprojectiles; and protoplast fusion. General transformationtechniques are known in the art (See, e.g., Ausubel et al., (1987),supra, chapter 9; and Sambrook (1989) supra, and Campbell et al., (1989)Curr. Genet. 16:53-56). The expression of heterologous protein inTrichoderma is described in U.S. Pat. No. 6,022,725; U.S. Pat. No.6,268,328; Harkki et al. (1991); Enzyme Microb. Technol. 13:227-233;Harkki et al., (1989) Bio Technol. 7:596-603; EP 244,234; EP 215,594;and Nevalainen et al., “The Molecular Biology of Trichoderma and itsApplication to the Expression of Both Homologous and HeterologousGenes”, in MOLECULAR INDUSTRIAL MYCOLOGY, Eds. Leong and Berka, MarcelDekker Inc., NY (1992) pp. 129-148). Reference is also made to Cao etal., (2000) Sci. 9:991-1001, EP 238023 and Yelton et al. (1984)Proceedings. Natl. Acad. Sci. USA 81:1470-1474 for transformation ofAspergillus strains.

Preferably, genetically stable transformants are constructed with vectorsystems whereby the nucleic acid encoding an asAA is stably integratedinto a host strain chromosome. Transformants are then purified by knowntechniques.

In one nonlimiting example, stable transformants including an amdSmarker are distinguished from unstable transformants by their fastergrowth rate and the formation of circular colonies with a smooth, ratherthan ragged outline on solid culture medium containing acetamide.Additionally, in some cases a further test of stability is conducted bygrowing the transformants on solid non-selective medium (i.e., mediumthat lacks acetamide), harvesting spores from this culture medium anddetermining the percentage of these spores which subsequently germinateand grow on selective medium containing acetamide. Alternatively, othermethods known in the art may be used to select transformants.

In one specific embodiment, the preparation of Trichoderma sp. fortransformation involves the preparation of protoplasts from fungalmycelia. (See, Campbell et al., (1989) Curr. Genet. 16:53-56). In someembodiments, the mycelia are obtained from germinated vegetative spores.The mycelia are treated with an enzyme that digests the cell wallresulting in protoplasts. The protoplasts are then protected by thepresence of an osmotic stabilizer in the suspending medium. Thesestabilizers include sorbitol, mannitol, potassium chloride, magnesiumsulfate and the like. Usually the concentration of these stabilizersvaries between 0.8 M and 1.2 M. It is preferable to use about a 1.2 Msolution of sorbitol in the suspension medium.

Uptake of DNA into the host Trichoderma sp. strain is dependent upon thecalcium ion concentration. Generally, between about 10 mM CaCl₂ and 50mM CaCl₂ is used in an uptake solution. Besides the need for the calciumion in the uptake solution, other compounds generally included are abuffering system such as TE buffer (10 Mm Tris, pH 7.4; 1 mM EDTA) or 10mM MOPS, pH 6.0 buffer (morpholinepropanesulfonic acid) and polyethyleneglycol (PEG). It is believed that the polyethylene glycol acts to fusethe cell membranes, thus permitting the contents of the medium to bedelivered into the cytoplasm of the Trichoderma sp. strain and theplasmid DNA is transferred to the nucleus. This fusion frequently leavesmultiple copies of the plasmid DNA integrated into the host chromosome.

Usually a suspension containing the Trichoderma sp. protoplasts or cellsthat have been subjected to a permeability treatment at a density of 105to 10⁷/mL, preferably 2×10⁶/mL are used in transformation. A volume of100 μL of these protoplasts or cells in an appropriate solution (e.g.,1.2 M sorbitol; 50 mM CaCl₂) are mixed with the desired DNA. Generally ahigh concentration of PEG is added to the uptake solution. From 0.1 to 1volume of 25% PEG 4000 can be added to the protoplast suspension.However, it is preferable to add about 0.25 volumes to the protoplastsuspension. Additives such as dimethyl sulfoxide, heparin, spermidine,potassium chloride and the like may also be added to the uptake solutionand aid in transformation. Similar procedures are available for otherfungal host cells. (See, e.g., U.S. Pat. Nos. 6,022,725 and 6,268,328,both of which are incorporated by reference).

Generally, the mixture is then incubated at approximately 0° C. for aperiod of between 10 to 30 minutes. Additional PEG is then added to themixture to further enhance the uptake of the desired gene or DNAsequence. The 25% PEG 4000 is generally added in volumes of 5 to 15times the volume of the transformation mixture; however, greater andlesser volumes may be suitable. The 25% PEG 4000 is preferably about 10times the volume of the transformation mixture. After the PEG is added,the transformation mixture is then incubated either at room temperatureor on ice before the addition of a sorbitol and CaCl₂ solution. Theprotoplast suspension is then further added to molten aliquots of agrowth medium. This growth medium permits the growth of transformantsonly.

Generally, cells are cultured in a standard medium containingphysiological salts and nutrients (See, e.g., Pourquie, J. et al.,BIOCHEMISTRY AND GENETICS OF CELLULOSE DEGRADATION, eds. Aubert, J. P.et al., Academic Press, pp. 71-86,1988 and Ilmen, M. et al., (1997)Appl. Environ. Microbiol. 63:1298-1306). Common commercially preparedmedia (e.g., Yeast Malt Extract (YM) broth, Luria Bertani (LB) broth andSabouraud Dextrose (SD) broth) also find use in the present invention.

Culture conditions are also standard, (e.g., cultures are incubated atapproximately 28° C. in appropriate medium in shake cultures orfermenters until desired levels of asAA expression are achieved).Preferred culture conditions for a given filamentous fungus are known inthe art and may be found in the scientific literature and/or from thesource of the fungi such as the American Type Culture Collection andFungal Genetics Stock Center.

After fungal growth has been established, the cells are exposed toconditions effective to cause or permit the expression of an asAA asdefined herein. In cases where an asAA having GSH activity codingsequence is under the control of an inducible promoter, the inducingagent (e.g., a sugar, metal salt or antimicrobial), is added to themedium at a concentration effective to induce asAA expression.

Identification of asAA Activity—

In order to evaluate the expression of an asAA having GSH activity by acell line that has been transformed with a heterologous polynucleotideencoding an asaA encompassed by the invention, assays can be carried outat the protein level, the RNA level or by use of functional bioassaysparticular to alpha amylase activity and/or production. In generalassays employed include, Northern blotting, dot blotting (DNA or RNAanalysis), RT-PCR (reverse transcriptase polymerase chain reaction), orin situ hybridization, using an appropriately labeled probe (based onthe nucleic acid coding sequence) and conventional Southern blotting andautoradiography.

In addition, the production and/or expression of an asAA having GSHactivity may be measured in a sample directly, for example, by assaysdirectly measuring reducing sugars such as glucose in the culture mediaand by assays for measuring glucoamylase activity, expression and/orproduction. Substrates useful for assaying GSH activity include granularstarch substrates. For example, glucose concentration may be determinedby any convenient method such as by using glucose reagent kit No 15-UV(Sigma Chemical Co.) or an instrument such as Technicon Autoanalyzer.Also reference is made to glucose oxidase kits and glucose hexose kitscommercially available from Instrumentation Lab. (Lexington, Mass.).

In addition, gene expression may be evaluated by immunological methods,such as immunohistochemical staining of cells, tissue sections orimmunoassay of tissue culture medium, e.g., by Western blot or ELISA.Such immunoassays can be used to qualitatively and quantitativelyevaluate expression of a asAA. The details of such methods are known tothose of skill in the art and many reagents for practicing such methodsare commercially available.

Alpha amylase activity may be measured by using the DNS method asdescribed in Miller, G. L. (1959) Anal. Chem. 31:426-428. Glucoamylaseactivity may be assayed by the 3,5-dinitrosalicylic acid (DNS) method(See, Goto et al., (1994) Biosci. Biotechnol. Biochem. 58:49-54).

In some embodiments of the invention, the asAA having GSH activityexpressed by a Trichoderma or Aspergillus host will be greater than 1gram protein per liter (g/L), greater than 2 g/L, greater than 5 g/L,greater than 10 g/L, greater than 20 g/L, greater than 25 g/L, greaterthan 30 g/L, greater than 50 g/L and also greater than 100 g/L ofculture media.

Methods for Purifying asAA—

In general, an asaA (including n-asAA or r-asAA) produced in cellculture is secreted into the medium and may be purified or isolated,e.g., by removing unwanted components from the cell culture medium. Insome cases, an AsaA may be produced in a cellular form necessitatingrecovery from a cell lysate. In such cases the enzyme is purified fromthe cells in which it was produced using techniques routinely employedby those of skill in the art. Examples include, but are not limited to,affinity chromatography (Tilbeurgh et al., (1984) FEBS Lett. 16:215);ion-exchange chromatographic methods (Goyal et al., (1991) Biores.Technol. 36:37; Fliess et al., (1983) Eur. J. Appl. Microbiol.Biotechnol. 17:314; Bhikhabhai et al., (1984) J. Appl. Biochem. 6:336;and Ellouz et al., (1987) Chromatography 396:307), includingion-exchange using materials with high resolution power (Medve et al.,(1998) J. Chromatography A 808:153; hydrophobic interactionchromatography (Tomaz and Queiroz, (1999) J. Chromatography A 865:123;two-phase partitioning (Brumbauer, et al., (1999) Bioseparation 7:287);ethanol precipitation; reverse phase HPLC; chromatography on silica oron a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE;ammonium sulfate precipitation; and gel filtration using, e.g., SephadexG-75.

Fermentations—

In some embodiments of the present invention, fungal cells expressing aheterologous asAA are grown under batch or continuous fermentationconditions. A classical batch fermentation is a closed system, whereinthe composition of the medium is set at the beginning of thefermentation and is not subject to artificial alterations during thefermentation. Thus, at the beginning of the fermentation the medium isinoculated with the desired organism(s). In this method, fermentation ispermitted to occur without the addition of any components to the system.Typically, a batch fermentation qualifies as a “batch” with respect tothe addition of the carbon source and attempts are often made atcontrolling factors such as pH and oxygen concentration. The metaboliteand biomass compositions of the batch system change constantly up to thetime the fermentation is stopped. Within batch cultures, cells progressthrough a static lag phase to a high growth log phase and finally to astationary phase where growth rate is diminished or halted. Ifuntreated, cells in the stationary phase eventually die. In general,cells in log phase are responsible for the bulk of production of endproduct.

A variation on the standard batch system is the “fed-batch fermentation”system, which also finds use with the present invention. In thisvariation of a typical batch system, the substrate is added inincrements as the fermentation progresses. Fed-batch systems are usefulwhen catabolite repression is apt to inhibit the metabolism of the cellsand where it is desirable to have limited amounts of substrate in themedium. Measurement of the actual substrate concentration in fed-batchsystems is difficult and is therefore estimated on the basis of thechanges of measurable factors such as pH, dissolved oxygen and thepartial pressure of waste gases such as CO₂. Batch and fed-batchfermentations are common and well known in the art.

Continuous fermentation is an open system where a defined fermentationmedium is added continuously to a bioreactor and an equal amount ofconditioned medium is removed simultaneously for processing. Continuousfermentation generally maintains the cultures at a constant high densitywhere cells are primarily in log phase growth.

Continuous fermentation allows for the modulation of one factor or anynumber of factors that affect cell growth and/or end productconcentration. For example, in one embodiment, a limiting nutrient suchas the carbon source or nitrogen source is maintained at a fixed rate anall other parameters are allowed to moderate. In other systems, a numberof factors affecting growth can be altered continuously while the cellconcentration, measured by media turbidity, is kept constant. Continuoussystems strive to maintain steady state growth conditions. Thus, cellloss due to medium being drawn off must be balanced against the cellgrowth rate in the fermentation. Methods of modulating is nutrients andgrowth factors for continuous fermentation processes as well astechniques for maximizing the rate of product formation are well knownin the art of industrial microbiology.

Compositions and Methods—

In one embodiment, a granular starch substrate is contacted with an asAAhaving GSH activity, wherein the asAA is available as a cell freefiltrate (for example wherein the asAA is isolated from a culturemedium). In another embodiment, the granular starch substrate iscontacted with an asAA having GSH activity, wherein the asAA isavailable in a culture medium containing the fungal host cells whichexpress and secret the asAA having GSH activity. In a further aspect,the invention encompasses a fermentation or culture medium comprising anacid stable alpha amylase (asAA) having granular starch hydrolyzingactivity produced from a culture of Trichoderma cells.

A particularly useful enzyme composition according to the invention is agranular starch hydrolyzing enzyme composition which includes an asAAhaving at least 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity toSEQ ID NO: 3. In some embodiments, the asAA is obtained from theheterologous expression of asAA and particularly the heterologousexpression of an Aspergillus kawachi acid stable alpha amylase in aTrichoderma or Aspergillus host. Another particularly useful enzymecomposition of the invention is a granular starch hydrolyzing enzymecomposition which comprises a truncated asAA having at least 97%, 98%and 99% sequence identity to the sequence of SEQ ID NO: 9.

In further embodiments, an enzyme composition according to the inventionwill include a combination of asAA enzymes having GSH activity whichinclude a) intact asAA having GSH activity which include a sequencehaving at least 85%, 90%, 95%, 96%, 97%, 98% and 99% identity to SEQ IDNO: 3 and b) a truncated asAA having GSH activity. In some embodimentsthe truncated asAA having GSH activity will be a sequence having atleast 96%, 97%, 98% and 99% sequence identity with the sequence of SEQID NO: 9.

In some embodiments the amount of intact asAA having GSH activitycompared to the total amount of asAA having GSH activity (intact plustruncated) in the enzyme composition will be at least about 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,and 98%. In other embodiments, ratio of intact asAA having GSH activityto truncated asAA having GSH activity in an enzyme composition accordingto the invention will be about 10% to 90%, 20% to 80%, 30% to 70%, 35%to 65%, 40% to 60%, 45% to 55%, 50% to 50%, 55% to 45%, 60% to 40%, 65%to 35%, 70% to 30%, 80% to 20% and 90% to 10% (intact to truncated). Insome preferred embodiments, the ratio will be between about 40% to 60%and about 60% to 40%.

In some embodiments, the amount of intact asAA to the total asAA will beat least about 70%, 80%, 85% and 90%. In other embodiments the ratio ofintact asAA to truncated asAA will be about 35% to 65% and also about40% to 60% (intact to truncated).

As understood by those in the art, the quantity of asAA having GSHactivity used in the compositions and methods of the present inventionwill depend on the enzymatic activity of the asAA. In some embodiments,the range of asAA present in the enzyme compositions is from 0.01 to 40SSU; 0.01 to 30 SSU; 0.01 to 20 SSU; 0.01 to 15.0 SSU and 0.01 to 10 SSUper g ds.

A particularly useful enzyme composition according to the invention is agranular starch hydrolyzing enzyme composition as disclosed above whichadditionally includes a glucoamylase.

Glucoamylases (GA) (E.C. 3.2.1.3) which may be useful in thecompositions and methods of the invention may be wild type orgenetically modified, including variants and hybrids. In general,glucoamylases. may be derived from bacteria, plants and fungal sources.Preferred glucoamylases useful in the compositions and methods of theinvention are produced by several strains of filamentous fungi andyeast. In particular, glucoamylases secreted from strains of Aspergillusand Trichoderma are commercially important. Sources of theseglucoamylases include: Aspergillus niger G1 and G2 glucoamylase andvariants thereof (Boel et al., (1984) EMBO J. 3:1097-1102; WO 92/00381;WO 00/04136 and U.S. Pat. No. 6,352,851); Aspergillus awamoriglucoamylases (WO 84/02921); Aspergillus oryzae glucoamylases andvariants thereof (Hata et al., (1991) Agric. Biol. Chem. 55:941-949) andAspergillus shirousami (See Chen et al., (1996) Prot. Eng. 9:499-505;Chen et al. (1995) Prot Eng. 8:575-582; and Chen et al., (1994) BiochemJ. 302:275-281). Glucoamylases are also obtained from strains ofTalaromyces such as those derived from T. emersonii, T. leycettanus, T.duponti and T. thermophilus (WO 99/28488; U.S. Pat. No. RE: 32,153; andU.S. Pat. No. 4,587,215); strains of Rhizopus, such as R. niveus and R.oryzae; strains of Mucor; strains of Trichoderma, such as T. reesei andT. viride and strains of Humicola, such as H. grisea (See, Boel et al.,(1984) EMBO J. 3:1097-1102; WO 92/00381; WO 00/04136; Chen et al.,(1996) Prot. Eng. 9:499-505; Taylor et al., (1978) Carbohydrate Res.61:301-308; U.S. Pat. No. 4,514,496; U.S. Pat. No. 4,092,434; and Jensenet al., (1988) Can. J. Microbiol. 34:218-223). Other glucoamylasesuseful in the present invention include those obtained from Atheliarolfsii and variants thereof (WO 04/111218).

Enzymes having glucoamylase activity used commercially are produced forexample, from Aspergillus niger (trade name DISTILLASE, OPTIDEX L-400and G ZYME G990 4X from Genencor International Inc.) or Rhizopus species(trade name CU.CONC from Shin Nihon Chemicals, Japan). Also thecommercial digestive enzyme, trade name GLUCZYME from AmanoPharmaceuticals, Japan (Takahashi et al., (1985) J. Biochem.98:663-671). Additional enzymes include three forms of glucoamylase(E.C.3.2.1.3) of a Rhizopus sp., namely “Gluc1” (MW 74,000), “Gluc2” (MW58,600) and “Gluc3” (MW 61,400). Gluc1 finds particular use in thepresent invention.

Some GA enzymes are also granular starch hydrolyzing enzyme(s) GSHE (Seee.g., Tosi et al., (1993) Can. J. Microbiol. 39:846-855). These GA-GSHEsnot only have glucoamylase activity, but also are able to hydrolyzegranular (raw) starch. GA-GSHEs have been recovered from fungal cellsand particularly filamentous fungal cells such as Humicola sp.,Aspergillus sp. Trichoderma sp. and Rhizopus sp. A Rhizopus oryzaeGA-GSHE has been described in Ashikari et al., (1986) Agric. Biol. Chem.50:957-964 and U.S. Pat. No. 4,863,864. Also reference is made toRhizopus niveus. A Humicola grisea GA-GSHE is described by Allison etal., (1992) Curr. Genet. 21:225-229, Tosi et al., (1993) Can. J.Microbiol. 39: 846-852, Campos et al., (1995) App. And Environ.Microbiol. 61:2436-2438 and European Patent No., 171218. The geneencoding this enzyme is also known in the art as “gla1”. An Aspergillusawamori var. kawachi GA-GSHE is described by Hayashida et al., (1989)Agric. Biol. Chem. 53:923-929. An Aspergillus shirousami GA-GSHE isdescribed by Shibuya et al., (1990) Agric. Biol. Chem. 54:1905-1914. Oneparticular GA-GSHE preparation for use in the present invention includesenzyme preparations sold under the designation “M1” available fromBiocon India, Ltd, India.

In some preferred embodiments, the glucoamylase is a GA-GSHE derivedfrom Trichoderma characterized by the protein sequence of SEQ ID NO:11or a sequence having at least 70%, 75%, 80%, 85%, 90%, 93%, 95%, 97%,98% and 99% sequence identity with SEQ ID NO:11.

In other preferred embodiments, the glucoamylase is a GA-GSHE derivedfrom an Aspergillus characterized by the protein sequence of SEQ ID NO:13 or a sequence having at least 70%, 75%, 80%, 85%, 90%, 93%, 95%, 97%,98% and 99% sequence identity with SEQ ID NO: 13.

In one embodiment, a GA-GSHE enzyme may be derived from a strain ofHumicola grisea, particularly a strain of H. grisea var. thermoidea(See, U.S. Pat. No. 4,618,579). In some preferred embodiments, theHumicola grisea GA-GSHE enzyme is recovered from fungi including ATCC16453, NRRL (USDA Northern Regional Research Laboratory, Peoria, Ill.)15219, NRRL 15220, NRRL 15221, NRRL 15222, NRRL 15223, NRRL 15224 andNRRL 15225, as well as genetically altered strains thereof. Thesespecies produce enzymatic glucoamylase preparations that areimmunologically the same (See, EP 0 171 218).

In other preferred embodiments the Humicola grisea GA-GSHE may have theprotein sequence of SEQ ID NO: 12 or a sequence having at least 70%,75%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity withSEQ ID NO: 12.

The glucoamylase may be supplied separately with an asAA having GSHactivity or the glucoamylase may be formulated with an asAA having GSHactivity according to the invention.

The amount of glucoamylase useful in an enzyme composition is in therange of 0.001 to 10.0 GAU/g ds, 0.01 to 10.0 GAU/g ds and also 0.1 to10.0 GAU/g ds. The activity of a GA-GSHE preparation may be defined interms of the glucoamylase activity.

In some embodiments the enzyme composition will include an asAA havingat least 85%, 90%, 95%, 98% or 99% sequence identity to SEQ ID NO: 3,wherein the asAA is obtained from the heterologous expression of asAAand particularly the heterologous expression of an Aspergillus kawachiasAA in a Trichoderma or an Aspergillus host and a glucoamylase. Theglucoamylase may be a wild type enzyme or it may be a variant GA orhybrid. In other embodiments, the enzyme composition will include acombination of a glucoamylase, intact asAA and truncated asAA as definedabove. In some preferred embodiments, the GA is obtained from anAspergillus strain, e.g., DISTILLASE®. In other embodiments, the GA isobtained from a Rhizopus, Trichoderma or Humicola strain. Morespecifically in some embodiments the asAA enzyme compositions will becombined with a glucoamylase which comprises an amino acid sequencehaving at least 90%, 95% and 98% sequence identity to the sequence ofSEQ ID NO: 11, SEQ ID NO: 12 or SEQ ID NO: 13.

While not meant to limit the invention, other particularly preferredenzyme compositions include the following combinations: a) aglucoamylase obtained from an Aspergillus niger and an asAA having GSHactivity having at least 95% sequence identity with SEQ ID NO: 3; b) aglucoamylase obtained from an Aspergillus niger and an asAA having GSHactivity having at least 96% sequence identity with SEQ ID NO: 9; c) aglucoamylase obtained from an Aspergillus niger, an asAA having GSHactivity having at least 95% sequence identity to SEQ ID NO: 3 and anasAA having at least 96% sequence identity with SEQ ID NO: 9; d) an asAAenzyme composition encompassed by the invention and a glucoamylasehaving an amino acid sequence of at least 90% sequence identity to SEQID NO: 11; e) an asAA enzyme composition encompassed by the inventionand a glucoamylase having an amino acid sequence of at least 90%sequence identity to SEQ ID NO: 12; and f) an asAA enzyme compositionencompassed by the invention and a glucoamylase having an amino acidsequence of at least 90% sequence identity to SEQ ID NO: 13.

Some particularly useful enzymatic compositions include a mixture of anasAA having at least 95% sequence identity to SEQ ID NO: 3 and a GAhaving 0.1 to 10 GAU/g ds. Another particularly useful enzymaticcomposition includes a mixture of an asAA having at least 98% sequenceidentity to SEQ ID NO: 3 and a GA having 0.1 to 10 GAU/g ds. Yet anotherparticularly useful enzymatic composition includes a mixture of an asAAhaving at least 98% sequence identity to SEQ ID NO: 9 and a GA having0.1 to 10 GAU/g ds. In some embodiments, the range of asAA present inthis mixture measured as activity is from 0.01 to 15.0 SSU.

In some embodiments, the ratio of asAA having GSH activity (SSU) to GAactivity (GAU) will be in the range of 40:1 to 1:40, also 30:1 to 1:30,also 20:1 to 1:20 and 15:1 to 1:15. In further embodiments, the ratio(SSU to GAU) will be in the range of about 20:1 to 1:10; about 10:1 to1:10; about 10:1 to 1:5; about 5:1 to 1:5, about 4:1 to 1:4; about 3:1to 1:3; about 2:1 to 1:4 and also about 2:1 to 1:2. In some preferredembodiments, the ratio of SSU to GAU will be between about 4:1 to 2:1.

In other embodiments, the asAA having GSH activity and the GA arepresent in a ratio such that the hydrolysis of granular starch in asubstrate is greater than the additive effect of the enzymes whensupplied at the same levels under the same conditions. In some cases thehydrolysis will be at least 1.0 times greater, at least 1.5 timesgreater, at least 2.0 times greater and also at least 3.0 times greater.The exact amounts of the components encompassed by the compositions ofthe invention will depend on the combination of enzymes.

In general, asAA having GSH activity will be mixed with a slurry of agranular starch substrate in an amount of about 0.01 to 15.0 SSU pergram of dry solids content of the slurry. In some embodiments, the asAAhaving GSH activity is added in an amount of about 0.01 to 10.0 SSU,about 0.01 to 5.0 SSU; about 0.05 to 10.0 SSU; about 0.05 to 5.0 SSU;about 0.1 to 10.0 SSU; about 0.1 to 5.0 SSU; about 0.1 to 2.0 SSU; about0.25 to 2.5 SSU; about 0.5 to 5.0 SSU; about 0.5 to 2.5 SSU; and alsoabout 0.5 to 1.5 SSU per gram of dry solids content of the slurry.

As understood by those in the art, the quantity of glucoamylase used inthe method and compositions of the present invention depends on theenzymatic activity of the glucoamylase. Generally, an amount of between0.001 and 10.0 GAU of glucoamylase per gram (ds) slurry adjusted to20-45% dry solids may be added. In some embodiments, the glucoamylase isadded in an amount between 0.01 and 10 GAU; between 0.01 and 5.0 GAU;between 0.05 and 5.0 GAU: between 0.1 and 10.0 GAU; between 0.1 and 5.0GAU; between 0.1 and 2.0 GAU; between 0.25 and 1.5 GAU of glucoamylaseper gram (ds) slurry. In one preferred embodiment, the dosage range forglucoamylase will be from 0.1 to 2.0 GAU/g (ds) slurry.

Additional enzymes may be included in the compositions and methodsencompassed by the invention. These additional enzymes, which find usein the present invention include debranching enzymes such aspullulanases (E.C. 3.2.1.41) and isoamylases (E.C. 3.2.1.68). Suchenzymes hydrolyze alpha-1,6-glucosidic bonds. Thus, during thehydrolysis of the starch, debranching enzymes remove successive glucoseunits from the non-reducing ends of the starch. Another enzyme that maybe used in the compositions of the invention are beta-amylases (E.C.3.2.1.2). These are exo-acting maltogenic amylases, which catalyze thehydrolysis of 1,4-alpha-glucosidic linkages in amylose, amylopectin andrelated glucose polymers. Some of these enzymes are characterized ashaving an optimum pH range from 4.5 to 7.0 and optimum temperature rangefrom 40° C. to 65° C. Commercial beta-amylases are available for exampleSPEMZYME BBA and OPTIMALT from Genencor International Inc.

Additional enzymes may include alpha amylases, which may or may not becharacterized by having GSH activity. Examples alpha amylases includeboth bacterial and fungal alpha amylases and variants thereof. Specificnot limiting examples include alpha amylases from Bacillusamyloliquefaciens, Bacillus stearothermophilus, B. licheniformis andvariants or hybrids thereof (U.S. Pat. No. 5,093,257; U.S. Pat. No.6,093,562; U.S. Pat. No. 5,736,499; U.S. Pat. No. 5,958,739; U.S. Pat.No. 6,436,888; U.S. Pat. No. 6,867,031; WO 96/39528; WO 96/23874 and WO05/001064). Commercially available alpha amylases are SPEZYME FRED andSPEZYME ETHYL (Genencor International Inc.). Cyclodextringlucanotransferases (CGTases) (E.C. 2.4.1.19) and variant thereof mayalso find use in the invention (U.S. Pat. No. 5,278,059; U.S. Pat. No.5,545,587 and WO 05/003337).

Further additional enzymes which may be used are proteases, such asfungal and bacterial proteases. Fungal proteases include for example,those obtained from Aspergillus, Trichoderma, Mucor and Rhizopus, suchas A. niger, A. awamori, A. oryzae and M. miehei. Other enzymes includebut are not limited to cellulases, such as endoglucanases;hemicellulases, such as mannases; lipases (e.g., E.C. 3.1.1.3), glucoseoxidases; pectinases; xylanases, cutinases (e.g., E.C. 3.1.1.74);transglucosidases and alpha 1,6 glucosidases (e.g., E.C. 3.2.1.20).

The effective amount of these enzymes to be included in the methods ofthe invention can be readily determined by one skilled in the art.

In some embodiments, an antimicrobial may be added to the compositionsand fermentation medium of the invention. Antimicrobials are compoundsthat kill or inhibit the growth of microorganisms.

Enzyme compositions comprising an asAA according to the invention mayinclude compositions for starch conversion and particularly granularstarch conversion, cleaning compositions, compositions for paper andpulp production, brewing compositions, baking compositions, compositionsfor textile applications, compositions for sweeteners and the like. Inone preferred embodiment, an enzyme composition comprising either anasAA alone or in combination with a glucoamylase will be used forproducing alcohol, e.g. ethanol. In some embodiments the ethanol will beproduced during a simultaneous saccharification and fermentation.

Methods:

In one embodiment, an enzyme composition comprising either an asaAhaving GSH activity alone or in combination with a glucoamylase will beadded to a slurry of a granular starch substrate and the mixture will befermented in a single step. The slurry may have about 10-50% ds; about10-45%; about 15-40%; about 20-40%; about 25-40%; or about 25-35% ds.

The exact amounts of the components encompassed by the composition andmethods of the invention depend on the combination of enzymes applied aswell as the type of granular starch processed.

In some embodiments the invention relates to a method of producing anend-product comprising contacting a slurry of a granular starchsubstrate with an enzyme composition comprising an acid stable alphaamylase (asAA) having granular starch (GSH) activity encompassed by theinvention in one-step to produce the end-product. In a preferredembodiment, the contacting step is conducted at a temperature below thestarch gelatinization temperature of the granular starch.

In a further embodiment the invention relates to a method of producingan end-product comprising contacting a slurry of a granular starchsubstrate with a combination of enzymes including glucoamylase and anacid stable alpha amylase (asAA) having granular starch (GSH) activityin one-step to produce the end-product. In some embodiments, the asAAand GA will be added separately and in other embodiments, the asAA andGA will be added in a combination blend. In a preferred embodiment, thecontacting step is conducted at a temperature below the starchgelatinization temperature of the granular starch.

The exact temperature used in accordance with the methods of theinvention depends upon the specific starch substrate used. Generalstarch gelatinization temperature ranges are disclosed in Swinkels pages32-38 in STARCH CONVERSION TECHNOLOGY, eds Van Beynum et al., (1985)Marcel Dekker Inc., NY and THE ALCOHOL TEXTBOOK, A REFERENCE FOR THEBEVERAGE, FUEL AND INDUSTRIAL ALCOHOL INDUSTRIES, 3^(rd) Ed., edsJacques et al., 1999, Nottingham University Press, UK. In someembodiments, the methods according to the invention will be conducted ata temperature of at least about 10° C., 15° C., 20° C., 25° C., 30° C.,35° C., 40° C., 45° C., 50° C., 55° C., 60° C., and 65° C. In otherembodiments, the temperature will be between about 25-65° C., about30-65° C., about 35-65° C., about 40-65° C., and about 45-65° C. Inother embodiments, the temperature will be between about 25-45° C.,about 25-40° C., about 30-40° C. and about 30-35° C. In preferredembodiments, the starch substrate is never subjected to the thermalconditions used for liquefactions.

In some embodiments, the methods according to the invention will beconducted at a pH of about pH 3.0 to 6.0; about pH 3.5 to 6.0; about pH3.5 to 5.5, about pH 3.5 to 5.0; and about pH 3.5 to 4.5.

In some embodiments, the residence time of the method is from about 2 to300 hrs, but more typically from 2 to 120 hours. In some embodiments,the process is conducted from about 5 to 100 hours. In otherembodiments, the process is conducted from about 5 to 80 hours. In stillother embodiments, the process is conducted for at least 5 hours butless than 100 hours.

In some embodiments, at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 94%,95%, 96%, 97%, 98% and 99% of the dry solids of the granular starch ishydrolyzed. In some embodiments, the granular starch substrate iscompletely hydrolyzed. In some embodiments, at least 90% of the granularstarch is hydrolyzed in 100 hours. In certain embodiments, at least 90%of the granular starch substrate is hydrolyzed in a time period of 24hours. In other embodiments, at least 95% of the granular starchsubstrate is hydrolyzed in a time period of 24 hours.

The yield of glucose (percent of the total solubilized dry solids) maybe at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97% and 98%.In some embodiments, the glucose. may be used to produce a high fructosesyrup (HFS). However, in a preferred embodiment, the glucose iscontinually produced and substantially all of the glucose is used in theprocess to produce an end-product, such as ethanol. (Reference is madeto MOLECULAR STRUCTURE AND FUNCTION OF FOOD CARBOHYDRATE, ED. G. G.BIRCH ET AL, APPLIED SCIENCE PUBLISHERS, LONDON). The glucose however,may be used to produce other end products including but not limited toorganic acids, amino acids, glycerol, ascorbic acid intermediates, (e.g.gluconate and 2,5-diketoglucoante) and other complex compounds such ashormones and antibiotics.

In another embodiment, the granular starch substrate may be pretreatedprior to contacting with the asAA and optionally the GA. Pretreatmentmay include exposing a granular starch substrate, preferably a slurrycontaining the raw substrate to a temperature below the starchgelatinization temperature of the starch substrate prior to thefermentation or culturing with an ethanologenic microorganism. Inpreferred embodiments, the pretreatment will include the use of an alphaamylase, such as a bacterial alpha amylase (i.e., SPEZYME and GZYME 997(Genencor International, Inc.) and optionally a cellulase (e.g.Cellulase 2000). In some embodiments, the pretreatment will be between40-65° C., also between 40-60° C., and between 42-52° C., at a pH rangeof 3.5 to 5.5, also between a pH of 3.5 to 5.0, between pH of 3.5 to 4.5and also between pH 3.8 to 4.2. In some embodiments, the pretreatmentwill be conducted for 30 minutes to 24 hours, also from 30 minutes to 12hours, also from 30 minutes to 8 hours, also from 30 minutes to 4 hoursand preferably from 1 hour to less than 3 hours.

In some embodiments, the pretreatment will be included in the culturewith an asAA having GSH activity according to the invention andoptionally with a glucoamylase. In other embodiments, the pretreatmentwill be separate from the culture which includes the asAA having GSHactivity and optionally the glucoamylase. In some embodiments thepretreatment will take place from about 1 to 24 hours, also 2 to 24hours. In other embodiments, the pretreatment will take place from about2 to 8 hours.

In some preferred embodiments, the method comprises a simultaneoussaccharification and fermentation (SSF), wherein the granular starchhydrolysis step and a fermentation step are carried outcontemporaneously. The culture medium, which includes the granularstarch substrate contacted with asAA having GSH activity, eithersupplied in a cell free filtrate or expressed from a fungal host cell inthe culture, will also include microorganisms, such as bacteria, fungalor yeast and particularly ethanologenic microorganisms. In someembodiments, the fermentation system may include at least two cellcultures. In some preferred embodiments, the SSF will include contactingthe granular starch substrate with a glucoamylase in addition to theasAA having GSH activity.

In some preferred embodiments the ethanologenic microorganisms willinclude yeast, such as Saccharomyces cerevisiae (U.S. Pat. No.4,316,956). Preferred examples of ethanologenic microorganisms alsoinclude bacteria expressing alcohol dehydrogenase and pyruvatedecarboxylase such as can be obtained with or from Zymomonas moblis(U.S. Pat. Nos. 5,028,539; 5,424,202; 5,487,989; 5,482,846; 5,554,520;and 5,514,583). In additional embodiments, the ethanologenicmicroorganisms express xylose reductase and xylitol dehydrogenase,enzymes that convert xylose to xylulose. Commercial sources of yeastinclude FALI; RED STAR (Red Star); FERMIOL (DSM Specialties) andSUPERSTART (Alltech).

In some embodiments, the residence time for the simultaneoussaccharification and fermentation will be from about 2 to 300 hours, butpreferably from 2 to 120 hours. In some embodiments, the time is fromabout 5 to 100 hours. In other embodiments, the time is from about 5 to80 hours. In still other embodiments, the time is for at least 5 hoursbut less than 100 hours. In other embodiments, the process time is forat least about 10 hours but less 100 hours at a temperature between10-40° C. and preferably between 25-40° C. and a pH of 3.5 to 6.0. Theuse of yeast in fermentation is well known and reference is made to THEALCOHOL TEXTBOOK, K. JACQUES ET AL., EDS. 1999, NOTTINGHAM UNIVERSITYPRESS, UK.

In some embodiments at least 5 vol %, at least 8 vol %, at least 10 vol%, at least 12 vol %, at least 15 vol % and at least 18 vol % of ethanolwill be produced in the fermentation media. In other embodiments, theamount of ethanol produced in the fermentation media will be between5-30%, also between 5-25%, and between 5-20%.

Following fermentation, alcohol (i.e., ethanol) may be recovered fromthe fermentation media by means known in the art. In some embodiments,the alcohol in the fermented medium may be distilled, for example byheating or vacuum distillation. The ethanol may then be used, forexample, as fuel ethanol or potable ethanol. The remaining residue,known as stillage may also be recovered and components of the stillagerecycled for the next fermentation or the stillage may be separated intoa soluble fraction or insoluble fraction.

When the stillage is separated for example by centrifugation orscreening into a soluble fraction and an insoluble fraction, thesefractions can be used to make distillers' solubles or distillers' driedsolubles or mixed together to make distillers' dried grain plus solubles(DDGS). One skilled in the art is familiar with processes for formingDDGS and distillers' grains in general. In some embodiments of theinvention, when % ethanol increases in the fermentation process, theamount of DDGS decreases. However, one significant advantage of themethod encompassed by the invention may be an increase in the % totalprotein in the DDGS and reference is made to example 10. The DDGS maythen be used for example, in an animal feed formulation.

In some embodiments, the SSF process encompassed by the invention willresult in a DDGS containing less than 30%, less than 15%, less than 10%,less than 9%, less than 8%, less than 7%, less than 6%, less than 5%,less than 4%, less than 2% and less than 1% residual starch. It iscontemplated that the DDGS which results from the process according tothe invention while having lower residual starch content compared toDDGS prepared by prior art processes will actually have an increasedtotal amount of protein and therefore be of additional benefit for usedin animal feeds.

The residual starch which is recovered from the fermentation may berecycled along with enzymes and/or microorganisms and subjected torenewed fermentation. In one embodiment, means for fermenting a granularstarch slurry of 20-50% ds contemporaneously with an asaA having GSHactivity and optionally a glucoamylase and microorganism will result inresidual starch when fermentation has proceeded to the intended alcoholcontent (e.g., 8 to 30%). The residual starch, the microorganisms and/orthe residual enzymes may be mixed with fresh granular starch andadditional aliquots of enzyme as needed to produce a fermentation chargefor another fermentation. However, it is not intended that the inventionbe limited to recycling the enzymes and/or microorganisms with theresidual starch. In some embodiments, the microorganisms are removedfrom the residual starch prior to recycling of the residual starch andin other embodiments, only the microorganisms are recycled. An exampleof the various embodiments presented herein is observed in FIG. 16.

While in preferred embodiments, the desired end-product is ethanol, thedesired end-product may be any product that may be produced by theenzymatic conversion of the granular starch substrate. Glucose obtainedfrom the hydrolysis of granular starch may be bioconverted into numerousproducts such as but not limited to ascorbic acid intermediates (e.g.,gluconate, 2-keto-L-gulonic acid, idonate, 5-keto-gluconate and2,5-diketogluconate); 1,3-propanediol; enzymes, aromatic amino acids(e.g. tyrosine, phenylalanine and tryptophan); organic acids (e.g.lactate, succinate, isocitrate and oxaloacetate); amino acids (serineand glycine); pyruvate and others. One skilled in the art is aware ofvarious fermentation conditions which may be used in the production ofthese end-products and enzyme assays to measure the levels of proteinexpression.

EXPERIMENTAL

The following examples are provided in order to demonstrate and furtherillustrate certain preferred embodiments and aspects of the presentinvention and are not to be construed as limiting the scope thereof.Indeed, it is contemplated that these teachings will find use in furtheroptimizing the process systems described herein.

In the disclosure and experimental section which follows, the followingabbreviations apply:

asAA having GSH activity (an acid-stable alpha amylase having granularstarch hydrolyzing activity); asaA (an acid-stable alpha amylase havinggranular starch hydrolyzing activity as illustrated in SEQ ID NO: 3 andwhich has been obtained from the endogenous expression of an asAA inAspergillus kawachi); Tr-asaA (the expression of the A. kawachiacid-stable alpha amylase expressed in a Trichoderma reesei host); AkM(the acid stable alpha amylase having SEQ ID NO: 3 and sometimes usedinterchangeability with asaA); GA (glucoamylase); HGA (a glucoamylasederived from a Humicola grisea having SEQ ID NO: 12); TrGA (aglucoamylase derived from a Trichoderma having SEQ ID NO: 11); wt %(weight percent); ° C. (degrees Centigrade); rpm (revolutions perminute); H₂O (water); dH₂O (deionized water); dIH₂O (deionized water,Milli-Q filtration); aa (amino acid); bp (base pair); kb (kilobasepair); kD (kilodaltons); g or gm (grams); μg (micrograms); mg(milligrams); μL (microliters); ml and mL (milliliters); mm(millimeters); μm (micrometer); M (molar); mM (millimolar); μM(micromolar); U (units); V (volts); MW (molecular weight); sec(seconds); min(s) (minute/minutes); hr(s) (hour/hours); PAGE(polyacrylamide gel electrophoresis); DO (dissolved oxygen); phthalatebuffer (sodium phthalate in water, 20 mM, pH 5.0); PBS (phosphatebuffered saline [150 mM NaCl, 10 mM sodium phosphate buffer, pH 7.2]);SDS (sodium dodecyl sulfate); Tris (tris(hydroxymethyl)aminomethane);w/v (weight to volume); w/w (weight to weight); v/v (volume to volume);Genencor (Genencor International, Inc., Palo Alto, Calif.); DDGS(Distilleries Dry Grain plus Solids); MT (Metric ton); and EtOH(ethanol).

The following assays and methods are used in the examples providedbelow:

Glucoamylase assay: Glucoamylase activity was measured using awell-known assay which is based on the ability of glucoamylase tocatalyze the hydrolysis of p-nitrophenyl-alpha-D-glucopyranoside (PNPG)to glucose and p-nitrophenol. At an alkaline pH, the nitrophenol; formsa yellow color that is proportional to glucoamylase activity and ismonitored at 400 nm and compared against an enzyme standard measured asa GAU.

One “Glucoamylase Activity Unit” (GAU) is defined as the amount ofenzyme that will produce 1 gm of reducing sugar, calculated as glucoseper hour from a soluble starch substrate (4% ds) at pH 4.2 and 60° C.

The measurement of acid-stable alpha amylase activity is based on thedegree of hydrolysis of soluble potato starch substrate (4% ds) by analiquot of the enzyme sample at pH 4.5, 50° C. The reducing sugarcontent is measured using the DNS method as described in Miller, G. L.(1959) Anal. Chem. 31:426-428. One unit of the enzyme activity (SSU,soluble starch unit) is equivalent to the reducing power of 1 mg ofglucose released per minute at the specific incubation conditions.

Determination of total starch content: The enzyme-enzyme starchliquefaction and saccharification process (dual enzyme method) was usedto determine the total starch content. In a typical analysis, 2 g of thedry sample was taken in a 100 ml Kohlraucsh flask and 45 ml of MOPSbuffer, pH 7.0 was added. The slurry was well stirred for 30 min.SPEZYME FRED (1:50 diluted in water), 1.0 ml was added and heated toboiling for 3-5 min. The flask was placed in an autoclave maintained at121° C. for 15 min. After autoclaving the flask was placed in a waterbath at 95° C. and 1 ml of 1:50 dilutes SPEZYME FRED was added andincubated for 45 min. The pH was adjusted to pH 4.2 and the temperaturewas reduced to 60° C. This was followed by addition of 20 ml acetatebuffer, pH 4.2. Saccharification was carried out by adding 1.0 ml of1:100 diluted OPTIDEX L-400 (Glucoamylase from Genencor InternationalInc.) and the incubation was continued for 18 hr at 60° C. The enzymereaction was terminated by heating at 95° C. for 10 min. The total sugarcomposition was determined by HPLC analysis using glucose as a standard.The soluble starch hydrolysate from water extraction of a sample at roomtemperature without enzymatic treatment was subtracted from the totalsugar.Residual starch iodine test: A sample of the beer (fermentation broth)was centrifuged in 2 ml plastic centrifuge tubes. The supernatant wasdecanted and the tube containing the pellet was placed in an ice bath.Several drops of 0.025N iodine solution (0.1N iodine from VWR Cat. No.VW3207-1 diluted 4×) was added to the pellet and mixed. A positive (+)starch shows a range of color from blue to purple and the intensity ofcolor is directly proportional to the concentration of starch. Anegative result (−) remains yellowish.Total protein analysis: The total nitrogen (N) in the samplepreparations was determined using the Kjeldhal method (American Assoc.Cereal Chemists (AACC), (1983), Methods 22B60 8th Ed. St Paul, Minn.).Protein content was calculated by 6.25× total N.

Ethanol and Carbohydrate Determinations:

Ethanol and carbohydrate composition of the samples were determinedusing the HPLC method as described herein:

a) a 1.5 mL Eppendorf centrifuge tube was filled with fermentor beer andcooled on ice for 10 min;b) the sample tube was centrifuged for 1 min in Eppendorf table topcentrifuge;c) a 0.5 mL sample of the supernatant was transferred to a test tubecontaining 0.05 mL of Kill solution (1.1N H₂SO₄) and allowed to standfor 5 min;d) 5.0 mL of water is added to the test tube sample and then filteredinto a HPLC vial through 0.45 μm Nylon Syringe Filter; and

e) run on HPLC. HPLC Conditions:

a) Ethanol System:

-   -   Column: Phenomenex Rezex Organic Acid Column        (RHM-Monosaccharide) #00H-0132-KO (Equivalent to Bio-Rad 87H)    -   Column Temperature: 60° C.    -   Mobile Phase: 0.01 N H₂SO₄    -   Flow Rate: 0.6 mL/min    -   Detector: RI    -   Injection Volume: 20 μL

b) Carbohydrate System:

-   -   Column: Phenomenex Rezex Carbohydrate (RCM-Monosaccharide)        #00H-0130-KO (Equivalent to Bio-Rad 87H)    -   Column Temperature: 70° C.    -   Mobile Phase: Nanopure DI H₂O    -   Flow Rate: 0.8 mL/min    -   Detector: RI    -   Injection Volume: 10 μL (3% DS material)        The column separates based on the molecular weight of the        saccharides, which are designated as DP1 (monosaccharides); DP2        (disaccharides); DP3 (trisaccharides) and DP+4 (oligosaccharide        sugars having a degree of polymerization greater than 3).        Preparation of asaA used in examples 7-16 was as follows. At the        end of the fermentation of the T. reesei which expresses asaA        (prepared according to examples 2 and 3), the biomass was        separated by centrifugation and the clear culture filtrate was        concentrated using a 10,000 molecular weight cut-off        ultrafiltration membrane. This ultrafiltrated concentrate having        (90 SSU/g) was used.        Preparation of glucoamylase used in examples 7-16 was as        follows: A selected fungal strain of Aspergillus niger as        described in U.S. Pat. No. 3,249,514 was used. After        fermentation, fungal mycelia were separated using conventional        separation methods including filtration and centrifugation. The        clear filtrate was concentrated by ultrafiltration at 5° C. to a        specified activity.

Example 1 Cloning the Aspergillus kawachi Acid-Stable Alpha-Amylase Gene

Genomic DNA was extracted from an overnight culture of A. kawachimycelia. The FastDNA Kit (QbioGene, Carlsbad, Calif.) SPIN™ protocol wasused according to the manufacturer's instructions for fungi. Forhomogenization, the sample was processed for 30 sec at speed 4.0 on aFastPrep Instrument. PCR primers were designed, based on the asaAsequence of A. Kaneko, et al. (Kaneko et al., (1996), J. Ferm Bioeng81:292-298). The forward primer contained a motif for directionalcloning into the pENTR/D vector (Invitrogen).

The sequence of the alpha6 primer was CACCATGAGAGTGTCGACTTCAAG (SEQ IDNO. 6) and the sequence of the Akaa3 primer was CTACCTCCACGTATCAACCAC(SEQ ID NO. 7).

The 2.36 kb PCR product was purified by gel extraction (Gel Purificationkit, Qiagen) and cloned into pENTR/D, according to the InvitrogenGateway system protocol. The vector was then transformed into chemicallycompetent Top10 E. coli (Invitrogen) with kanamycin selection. PlasmidDNA from several clones was digested with restriction enzymes to confirmthe correct size insert. The alpha-amylase gene insert was sequenced(Sequetech, Mountain View, Calif.) from several clones (SEQ ID NO:1).Plasmid DNA from one clone, pENTR/D_Akaa#11, was added to the LR clonasereaction (Invitrogen Gateway system) with pTrex3g/amdS destinationvector DNA. Recombination, in the LR clonase reaction, replaced the CmRand ccdB genes of the destination vector with the A. kawachi asaA fromthe pENTR/D vector. This recombination directionally inserted asaAbetween the cbhI promoter and terminator of the destination vector.Recombination site sequences of 48 and 50 bp remained upstream anddownstream, respectively, of the alpha amylase. An aliquot of the LRclonase reaction was transformed into chemically competent Top10 E. coliand grown overnight with carbenicillin selection. For removal of thefungal cassette from the bacterial plasmid, the Stratagene QuickChangeprotocol was followed to add an EcoRI site 3′ to the amdS gene. Thesequence of the fungal expression cassette was confirmed. Plasmid DNAfrom several clones was restriction digested to confirm the correctinsert size. Plasmid DNA from clone, pTrex3g_Akalpha#1 (FIG. 4) wasdigested with EcoRI to release the expression cassette including thecbhI promoter:asaA:cbhI terminator:amdS. This 7.8 kb cassette waspurified by agarose extraction using standard techniques and transformedinto a strain of T. reesei derived from the publicly available strainQM6a, as further described below.

Example 2 Biolistic Transformation of T. reesei

A Trichoderma reesei spore suspension was spread onto the center ˜6 cmdiameter of an MABA transformation plate (150 μl of a 5×10⁷-5×10⁸spore/ml suspension). The plate was then air dried in a biological hood.The stopping screens (BioRad 165-2336) and macrocarrier holders (BioRad1652322) were soaked in 70% ethanol and air dried. DriRite desiccant wasplaced in small Petri dishes (6 cm Pyrex) and overlaid with Whatmanfilter paper. The macrocarrier holder containing the macrocarrier(BioRad 165-2335) was placed flatly on top of filter paper and the Petridish lid replaced.

A tungsten particle suspension was prepared by adding 60 mg tungstenM-10 particles (microcarrier, 0.7 micron, BioRad #1652266) to anEppendorf tube. 1 ml ethanol (100%) was added. The tungsten was votexedin the ethanol solution and allowed to soak for 15 minutes. TheEppendorf tube was microfuged briefly at maximum speed to pellet thetungsten. The ethanol was decanted and washed three times with steriledistilled water. After the water wash was decanted the third time, thetungsten was resuspended in 1 ml of sterile 50% glycerol. The tungstenwas prepared fresh at least every two weeks.

The transformation reaction was prepared by adding 25 μl of suspendedtungsten to a 1.5 ml Eppendorf tube for each transformation. Subsequentadditions were made in order, 0.5-5 μl DNA (XbaI-digested expressioncassette), 25 μl 2.5M CaCl₂, 10 μl 0.1 M spermidine. The reaction wasvortexed continuously for 5-10 minutes, keeping the tungsten suspended.The Eppendorf tube was then microfuged briefly and decanted. Thetungsten pellet was washed with 200 μl of 70% ethanol, microfugedbriefly to pellet and decanted. The pellet was washed with 200 μl of100% ethanol, microfuged briefly to pellet, and decanted. The tungstenpellet was resuspended in 24 μl 100% ethanol. The Eppendorf tube wasplaced in an ultrasonic water bath for 15 seconds and 8 μl aliquots weretransferred onto the center of the desiccated macrocarriers. Themacrocarriers were left to dry in the desiccated Petri dishes.

A He tank was turned on to 1500 psi. 1100 psi rupture discs (BioRad165-2329) were used in the Model PDS-1000/He Biolistic Particle DeliverySystem (BioRad). When the tungsten solution was dry, a stopping screenand the macrocarrier holder were inserted into the PDS-1000. An MABAplate, containing the target T. reesei spores, was placed 6 cm below thestopping screen. A vacuum of 29 inches Hg was pulled on the chamber andheld. The He Biolistic Particle Delivery System was fired. The chamberwas vented and the MABA plate removed for incubation at 28° C. untilcolonies appeared (5 days).

With reference to this Example 2 the following solutions were prepared,

Modified amdS Biolistic agar (MABA) per liter Part I, make in 500 mldH₂O 1000× salts 1 ml Noble agar 20 g pH to 6.0, autoclave Part II, makein 500 ml dH₂O Acetamide 0.6 g CsCl 1.68 g Glucose 20 g KH₂PO₄ 15 gMgSO₄•7H₂O 0.6 g CaCl₂•2H₂O 0.6 g pH to 4.5, 0.2 micron filtersterilize; leave in 50° C. oven to warm, add to agar, mix, pour plates.Stored at room temperature.

1000× Salts per liter FeSO₄•7H₂O  5 g MnSO₄•H₂O 1.6 g ZnSO₄•7H₂O 1.4 gCoCl₂•6H₂O  1 g Bring up to 1 L dH₂O. 0.2 micron filter sterilize

Example 3 PEG-Mediated Protoplast Fusion Transformation of T. reesei

A 1-2 cm² agar plug of a sporulated mycelia (grown on potato dextroseagar (PDA), Difco for 5 days at 30° C.) was inoculated into 50 ml of YEG(5 g/L yeast extract plus 20 g/L glucose) broth in a 250 ml, 4-baffleshake flask and incubated at 30-37° C. for 16-20 hours at 200 rpm. Themycelia were recovered by transferring the shake flask contents into 50ml conical tubes and spinning at 2500 rpm for 10 minutes. Thesupernatant was discarded and the mycelial pellet was transferred into a250 ml, 0.22 m CA or PES Corning filter bottle containing 40 ml offiltered β-D-glucanase solution. The solution was incubated at 30° C.,200 rpm, for 2 hours to generate protoplasts. Protoplasts were harvestedby filtration, through sterile Miracloth (CalBiochem, La Jolla, Calif.),into a 50 ml conical tube. The protoplasts were pelleted bycentrifugation at 2000 rpm for 5 minutes and the supernatant discarded.Protoplast pellets were washed once with 50 ml of 1.2 M sorbitol;centrifuged (2000 rpm, 5 min.) and supernatant was discarded. The pelletwas washed with 25 ml of sorbitol/CaCl₂. A haemocytometer was used tocount the protoplasts and then pelleted by centrifugation at 2000 rpmfor 5 min. The supernatant was discarded and protoplast pelletsresuspended in a volume of sorbitol/CaCl₂ sufficient to generate aprotoplast solution with a protoplast concentration of 1.25×10⁸/ml.

For each transformation, an aliquot of 20 μg of expression vector DNA(in a volume no greater than 20 μl) was transferred into 15 ml conicaltubes, on ice. Protoplast suspension (200 μl) and 50 μl PEG solution wasadded to each tube. This was mixed gently and incubated on ice for 20min. PEG (2 ml) solution was added to each transformation tube andincubated at room temperature for 5 minutes. 4 ml sorbitol/CaCl₂solution was added to each tube (total volume 6.2 ml) and mixed gently.Then 2 ml of the transformation mixture was added to each of 3 molten(50° C.) top agar tubes. Each top agar mixture was poured onto aseparate transformation plate and incubated at 30° C. for four to sevendays.

For transformation with amdS selection, acetamide/sorbitol plates andtop agar were used. Selection plates were the same as transformationplates, but without sorbitol. Putative transformants were purified bytransferring isolated colonies to fresh selective media containingacetamide.

Media and solutions were prepared as follows.

-   -   1) 40 ml β-D-glucanase solution—dissolved 600 mg β-D-glucanase        (InterSpex Products Inc., San Mateo, Calif.) and 400 mg        MgSO₄.7H₂O in 40 ml 1.2M sorbitol.    -   2) 200 ml PEG mix—Dissolved 50 g PEG 4000 (BDH Laboratory        Supplies Poole, England) and 1.47 g CaCl₂.2H₂O in 200 ml dIH₂O.        Prepared fresh monthly.    -   3) Sorbitol/CaCl₂ solution—Dissolved 50 mM CaCl₂ in 1.2M        sorbitol.    -   4) Acetamide/sorbitol agar—        -   Part 1—Dissolved 0.6 g acetamide (Aldrich, 99% sublime.),            1.68 g CsCl, 20 g glucose, 20 g KH₂PO₄, 0.6 g MgSO₄.7H₂O,            0.6 g CaCl₂.2H₂O, 1 ml 1000× salts (see below) in 200 ml            dIH₂O, adjusted to pH 5.5, brought volume up to 300 mls with            dH₂O, and filter sterilized.        -   Part II—20 g Noble agar and 218 g sorbitol were added to a 1            L cylinder, brought to volume (700 mls) with dIH₂O, and            autoclaved.        -   Part II was added to Part I for a final volume of 1 L.    -   5) 1000× Salts—Combined 5 g FeSO₄.7H₂O, 1.6 g MnSO₄H₂O, 1.4 g        ZnSO₄.7H₂O, 1 g CoCl₂.6H₂O and brought the volume up to 1 L with        dIH₂O. Filter sterilized.

Example 4 PEG-Mediated Protoplast Fusion Transformation of Aspergillusniger

A 2 cm² agar plug was inoculated from a sporulated A. niger plate, into50 ml of YEG (5 g/L yeast extract plus 20 g/L glucose) broth in a 250ml, 4-baffle shake flask. The agar plug was incubated at 30′-37° C. for16-20 hours at 200 rpm, mycelia was harvested through a sterileMiracloth filter and washed with Solution A. Washed mycelia wasaseptically transferred into 40 ml of protoplasting solution andincubated at 30° C., 200 rpm, for 1-2 hours, protoplasting progress wasmonitored microscopically. The protoplasting reaction was filteredthrough sterile Miracloth, into two 50 ml sterile disposable centrifugetubes and the volume brought up to 45 mls each with Solution B. Theprotoplasts were centrifuged at 2500 rpm for 5 minutes to obtain pelletsand the supernatant was discarded. The pellet was washed twice more with20 ml volumes of Solution B. The pellet was resuspended in 10 mlSolution B and protoplasts counted using a haemocytometer. Protoplastswere again centrifuged and the supernatant discarded. Protoplasts wereresuspended, in Solution B to yield ˜1×10⁷/100 μl. On ice, 100 μlprotoplast solution was added to pre-chilled 15 ml tubes, one tube pertransformation. 10 μg DNA was added in a volume not exceeding 10 μl.Solution C (12.5 μl) was added, mixed gently, and incubated on ice for20 minutes.

MMS top agar (3 tubes of 10 ml each, per transformation) was melted andmaintained at 55° C. Protoplasts were removed from the ice and SolutionC (1 ml) and Solution B (2 ml) were added to each tube and the tubeswere mixed gently. 1 ml of the protoplast mixture was added to each ofthe 3 top agar tubes and the top agar was poured onto MMS plates. Thiswas repeated for each transformation and plates were incubated for 4-7days at 30° C.

Solution A (per 500 ml)—0.44 g K₂HPO₄; 0.34 g KH₂PO₄; 48.156 g anhydrousMgSO₄ (FW 120.37); and dIH₂O added for a final volume of 500 ml, pH 5.5.Filter sterilized and stored at room temperature.Protoplasting solution—Dissolved 180 units beta-D-glucanase (InterSpexProducts, Inc) in 40 ml Solution A. Filter sterilized, 0.2 micron.Solution B (per 500 ml)—5 ml 1M Tris, pH 7.5; 2.77 g CaCl₂ (FW 110.99);109.32 g Sorbitol (FW 182.2; 1.2M); and dIH₂O added for a final volumeof 500 ml.Filter sterilized and stored at room temperature.Solution C (per 500 ml)—2509 PEG 4000; 2.77 g CaCl₂; 5 ml 1M Tris, pH7.5; and dIH₂O added for a final volume of 500 ml. Filter sterilized.MMS Agar*—Dissolved in 1 L dIH₂O,6 g/L NaNO₃; 0.52 g/L KCl; 1.52 g/L KH₂PO₄; 218.5 g/L D-Sorbitol; 1 ml/LTrace elements (see below); 10 g/L agar (low melt agarose in the topagar). *For amdS selection, replace the nitrate in the MMS with 0.59 g/Lacetamide and 3.4 g/L CsCl.Autoclave. Post-sterilization, aseptically added 10 ml 50% glucose and1.25 ml 20% MgSO₄.7H₂0.

Trace Elements Solution

Dissolve in 250 ml dIH₂O,

1 g/L FeSO₄.7H₂O 8.8 g/L ZnSO₄.7H₂O 0.4 g/L CuSO₄.5H₂O 0.15 g/LMnSO₄.4H₂O 0.1 g/L Na₂B₄O₇.10H₂O

50 mg/L (NH₄)₆Mo₇O₂₄.4H₂OMix and added 0.2 ml concentrated HCl to dissolve. Brought volume up to1 L with dIH₂O. Filter sterilized.

Example 5 Fermentation of T. reesei Transformed with the asaA Gene andAssay of Activity in T. reesei Clones

In general, the fermentation protocol as described in Foreman et al.(Foreman et al. (2003) J. Biol. Chem. 278:31988-31997) was followed.More specifically, duplicate fermentations were run for each of thestrains displayed in FIG. 5A. 0.8 L of Vogels minimal medium (Davis etal., (1970) METHODS IN ENZYMOLOGY 17A, pg 79-143 and Davis, Rowland,NEUROSPORA, CONTRIBUTIONS OF A MODEL ORGANISM, Oxford University Press,(2000)) containing 5% glucose was inoculated with 1.5 ml frozen sporesuspension. After 48 hours, each culture was transferred to 6.2 L of thesame medium in a 14 L Biolafitte fermenter. The fermenter was run at 25°C., 750 RPM and 8 standard liters per minute airflow. One hour after theinitial glucose was exhausted, a 25% (w/w) lactose feed was started andfed in a carbon limiting fashion to prevent lactose accumulation. Theconcentrations of glucose and lactose were monitored using a glucoseoxidase assay kit or a glucose hexokinase assay kit withbeta-galactosidase added to cleave lactose, respectively(Instrumentation Laboratory Co., Lexington, Mass.). Samples wereobtained at regular intervals to monitor the progress of thefermentation. Collected samples were spun in a 50 ml centrifuge tube at¾ speed in an International Equipment Company (Needham Heights, Mass.)clinical centrifuge. Sample supernatants were run of 4-12% BIS-TRISSDS-PAGE gels, under reducing conditions with MOPS(morpholinepropanesulfonic acid) SDS running buffer and LDS samplebuffer (FIG. 5A).

In additional fermentations, sample supernatants were run as basicallydescribed above. However, different proportions of intact and truncatedforms of Tr-asaA were obtained. FIG. 5B, lane 2 illustrates three majorbands between 50 and 90 kD. The three bands from the gel were digestedusing modified methods known in the art (Hellman et al., (1995) Anal.Biochem. 224:451-455). Peptides were extracted, separated using reversephase HPLC and peptide mass and ms/ms fragmentation patterns determined.The resulting peptide maps confirmed that both lower MW bands weretruncated. One band represented a truncated asAA in which clippingoccurred between amino acid position 434 and 580 of SEQ ID NO: 3 and thesecond band represented a truncated asAA in which clipping took place atabout amino acid position 581 of SEQ ID NO: 3. Each band exhibited alphaamylase and GSH activity.

Example 6 Comparison of pH Stability of Native and Recombinant A.kawachi Acid-Stable Alpha Amylase Having GSH Activity (asaA)

Samples of recombinantly produced asaA (Tr-asaA) as described above andsamples of native asaA were diluted to equal protein concentrations with20 mM acetate buffer at pH 4.5. Reactions were run in 100 mMcitrate/NaOH buffers at 50° C. for 30 minutes at pH levels 3 to 7. 1.0mL of the reaction was added to 5 mL of 10% corn starch (Cargill Foods,MN) in 100 mM acetate, pH 4.5 in sample tubes. The tubes were shaken at50° C. for 20 minutes. Then 0.5 mL 2.0% NaOH was added. Tubes were spunand 0.5 mL of the supernatant were assayed for reducing sugars using theDinito Salicylic Acid (DNS) Assay (Goto et al., (1994) supra). Theresults are depicted in FIG. 6. The r-asaA exhibited 100% residualactivity at pH 3.9. In comparison the n-asaA exhibited 100% residualactivity at pH 4.5.

Example 7 Effect of Tr-asaA Concentrations During SimultaneousSaccharification and Fermentation (SSF) of Non-Cooked Whole Ground CornSubstrate

Tr-asaA was evaluated at two levels of glucoamylase (GA) from a cellfree culture filtrate (0.5 and 1.0 GAU/g). Thirty six percent corn flourslurry was prepared containing dry corn steep (2.5% of corn flour). ThepH of the slurry was adjusted to 4.8 with dilute sulfuric acid. Thetotal dry solids of the slurry were 33.85%. Fermentations were carriedout in 125 ml flasks containing 100 gm of mash (slurry). The desiredlevels of enzymes were added then 3 ml of propagated yeast slurry wasadded to start the fermentation. The yeast inoculum was prepared byadding 0.26 gm of dry Fali yeast to 100 gm of mash containing GAactivity at 0.9 GAU/g of raw material solids. This slurry was placed ina 32° C. water bath and gently mixed for about 17 hours. At various timeintervals samples of the fermentation (beer) were taken for HPLCanalysis. After 72 hours the fermentations was terminated and the beerwas dried at 60° C. to obtain the DDGS.

The starch content of the DDGS was determined and the insoluble solidsof the beer after terminating the fermentation were spot checked forstarch by the addition of Iodine. The enzymes used in this study were A.niger GA. Table 1 summarizes ethanol levels, iodine stain of the mashsolids and % starch of the DDGS.

TABLE 1 Effect of asaA During Conversion of Granular Corn Starch toEthanol under Yeast Fermentation Conditions GA asaA % v/v % v/v % v/v %GAU/ SSU/ EtOH EtOH EtOH starch g ds g ds 24 hr 50 hr 72 hr DDGS Iodine0.5 7.7 11.4 13.7 27.4 + 0.5 0.25 9.2 14.7 16.9 7.7 + 0.5 0.50 9.6 15.417.0 5.7 +/−  0.5 1.0 10.0 16.2 17.3 4.1 +/−− 0.5 2.0 10.9 16.5 17.5 2.8− 0.5 3.0 11.2 16.8 17.5 1.6 − 0.5 4.0 11.2 16.9 17.4 1.7 − 0.5 5.0 11.217.0 17.7 1.5 − 1.0 9.3 14.4 16.2 13.0 + 1.0 0.25 11.6 17.1 17.8 3.6+/−− 1.0 0.5 12.1 16.8 17.9 2.6 − 1.0 1.0 12.7 17.2 17.7 2.2 − 1.0 2.012.7 17.6 17.8 1.6 − 1.0 3.0 12.9 17.5 17.8 1.1 − 1.0 4.0 13.2 17.5 17.90.8 − 1.0 5.0 13.3 17.2 17.9 1.1 − 2.0 11.2 15.5 16.9 9.6 + 3.0 11.415.9 17.2 5.8 +

Example 8 Conversion of Granular Starch Substrates by Glucoamylase andAlpha Amylases

Commercial alpha amylases from different sources were compared withTr-asaA under the simultaneous saccharification and fermentationconditions in the presence of glucoamylase at 0.5 GAU/g of ds. Theactivity of the commercial alpha amylases was determined using thesoluble starch substrate (SSU) method assay as described earlier.

TABLE 2 Alpha Amylase Microbial Strain SSU/ml Tr-asaA A. kawachi asAAexpressed 90 in T. reesei SPEZYME LT AA Bacillus amyloliquefaciens 2,759SPEZYME FRED Bacillus licheniformis** 4,842 SPEZYME Ethyl Bacillusstereothermophilus** 22,082 CLARASE L Aspergillus oryzae 23,087**denotes a recombinant strain

Ethanol fermentation was carried out using whole ground corn asdescribed in Example 7. Alpha amylases from the sources listed in Table2 were added at 1.0 SSU/gram of ground corn and glucoamylase at 0.5GAU/g. The samples were taken during the course of the fermentation andanalyzed for ethanol content (FIG. 7). After the fermentation, theinsoluble solids (DDGS) were separated and the residual starch contentof the corn mash at pH 5.0 was determined. The results are summarized inTable 3.

TABLE 3 Ave % v/v EtOH Residual % GAU/g Alpha Amylase at starch in DDGSds (1.0 SSU/g ds) 22 hr 46 hr 72 hr 72 hr 0.5 — 7.77 11.56 14.44 29.80.5 SPEZYME LT-AA 7.72 11.56 14.78 30.8 0.5 SPEZYME FRED 7.84 11.7714.59 30.8 0.5 SPEZYME Ethyl 7.94 11.82 14.57 29.1 0.5 CLARASE L 7.9411.72 14.62 30.8 0.5 Tr-asaA 9.57 15.75 18.44 9.0

The results in Table 3 clearly show that Tr-asaA is very effective inaiding glucoamylase to hydrolyze granular starch under the ethanolfermentation conditions using yeast. Additionally, as observed from thetable, % ethanol produced in the fermentation (18.44) is greater and %residual starch in DDGS (9.0) is significantly lower using the enzymecombination of the present invention.

Example 9 Evaluation of Whole Ground Wheat in the Ethanol FermentationUsing Tr-asaA

To a 36% slurry of whole ground wheat, dry corn steep liquor was addedat 2.5% based on the weight of the whole ground wheat. The fermentationswere carried out in 125 ml flasks containing 100 gm of mash. The pH ofthe slurry was adjusted to 4.8 with dilute sulfuric acid. The mash wasdiluted to a final concentration of 33.85% ds.

Glucoamylase (0.5 GAU/g ground wheat) and asaA (1.0 SSU/g whole groundwheat) were added to the mash. This was followed by adding 3.0 ml ofpropagated yeast to start the fermentation. Yeast inoculum was preparedby adding 0.26 gm of dry Fali yeast to 100 gm of mash. The fermentationswere run in a 32° C. water bath while gently stirred. At various timeintervals samples of the fermentation broth (beer) were taken,centrifuged for HPLC analysis of sugar composition and ethanol (Table4).

TABLE 4 Whole ground wheat granular starch in the yeast fermentation forethanol production GA Tr-asaA % w/v % w/v % w/v % w/v % w/v % v/v GAU/gds SSU/g ds Hrs DP > 2 DP-2 DP-1 Lactic Glycerol Ethanol 0 0.98 0.972.00 0.22 0.12 0.00 0 0 24 1.33 0.00 0.02 1.09 0.15 2.42 0 0 48 1.170.00 0.00 1.39 0.13 2.38 0 0 72 1.08 0.00 0.01 1.38 0.13 2.16 0 0.1 241.30 0.00 0.02 1.06 0.16 4.49 0 0.1 48 1.16 0.00 0.02 1.51 0.16 2.28 00.1 72 1.23 0.00 0.01 1.83 0.15 2.91 0 0.25 24 1.28 0.03 0.02 1.06 0.172.94 0 0.25 48 1.05 0.00 0.02 1.41 0.15 2.73 0 0.25 72 1.24 0.00 0.031.92 0.17 3.06 0 0.5 24 1.25 0.00 0.01 1.02 0.13 3.03 0 0.5 48 1.22 0.000.02 1.60 0.18 3.27 0 0.5 72 1.26 0.00 0.03 1.90 0.18 3.24 0 0.75 241.29 0.03 0.02 1.06 0.16 3.21 0 0.75 48 1.29 0.00 0.03 1.62 0.10 3.57 00.75 72 1.34 0.00 0.03 1.90 0.18 3.60 0 1.0 24 1.29 0.04 0.02 1.04 0.163.43 0 1.0 48 1.32 0.04 0.01 1.55 0.18 4.02 0 1.0 72 1.46 0.09 0.04 1.841.21 4.15 0.2 0 24 1.18 0.00 0.00 1.04 0.18 3.34 0.2 0 48 1.16 0.00 0.021.67 0.19 4.14 0.2 0 72 1.16 0.00 0.02 1.92 0.19 4.78 0.2 0.1 24 1.200.00 0.03 1.05 0.20 3.64 0.2 0.1 48 1.12 0.00 0.02 1.59 0.20 4.60 0.20.1 72 1.14 0.00 0.03 1.86 0.21 5.58 0.2 0.25 24 1.16 0.00 0.03 1.020.21 3.80 0.2 0.25 48 1.14 0.00 0.03 1.57 0.22 5.13 0.2 0.25 72 1.060.03 0.03 1.71 0.21 5.90 0.2 0.5 24 1.20 0.00 0.03 1.03 0.22 4.04 0.20.5 48 1.14 0.00 0.01 1.54 0.22 5.61 0.2 0.5 72 1.13 0.03 0.04 1.74 0.236.65 0.2 0.75 24 1.16 0.00 0.03 1.03 0.22 4.13 0.2 0.75 48 1.24 0.000.04 1.54 0.24 5.68 0.2 0.75 72 1.10 0.00 0.01 1.63 0.23 7.14 0.2 1.0 241.00 0.00 0.03 0.96 0.17 4.14 0.2 1.0 48 1.16 0.00 0.04 1.50 0.25 5.900.2 1.0 72 1.21 0.03 0.04 1.68 0.23 6.76 0.5 0 24 1.07 0.00 0.03 0.980.24 4.50 0.5 0 48 1.01 0.00 0.02 1.41 0.25 6.29 0.5 0 72 1.10 0.03 0.151.55 0.25 7.49 0.5 0.1 24 1.12 0.00 0.04 0.94 0.24 4.62 0.5 0.1 48 1.120.00 0.03 1.34 0.27 6.92 0.5 0.1 72 1.09 0.03 0.03 1.46 0.27 8.45 0.50.25 24 1.17 0.00 0.05 0.97 0.27 5.01 0.5 0.25 48 1.20 0.00 0.04 1.280.28 7.18 0.5 0.25 72 1.06 0.03 0.03 1.34 0.27 8.78 0.5 0.5 24 1.16 0.000.05 0.91 0.26 5.29 0.5 0.5 48 1.11 0.00 0.04 1.18 0.28 7.71 0.5 0.5 721.07 0.03 0.04 1.23 0.28 9.47 0.5 0.75 24 1.15 0.00 0.05 0.90 0.28 5.330.5 0.75 48 1.11 0.03 0.06 1.16 0.30 8.08 0.5 0.75 72 1.06 0.04 0.051.17 0.30 9.91 0.5 1.0 24 1.12 0.00 0.06 0.89 0.29 5.52 0.5 1.0 48 1.120.00 0.05 1.14 0.32 8.39

Example 10 Effect of Substrate Treatment on the Ethanol Yield andComposition of Distilleries Dry Grain Solids, (DDGS)

Whole ground corn substrate was subjected to a conventional dry millingprocess for fuel alcohol fermentation using a hammer mill to reduceparticle size. Three different mashes were prepared.

Treatment 1 (Trt 1) is a high temperature treatment, which involved abatch liquefaction of a 36% ds corn flour slurry containing 0.9% drycorn steep (DCS) with 3.5 U/g SPEZYME ETHYL at pH 5.6 by jet cookingaccording to the prior art procedures. The slurry was place in a 90° C.bath for 1.5 hours, mixed and then cooled to 30° C. with a pH adjustmentto 5.0 with dilute sulfuric acid. The slurry was further diluted withwater to 32.71% ds.

Treatment 2 (Trt 2) is a low temperature treatment. The mash wasprepared by incubating a 36% corn flour slurry containing 0.9% DCS withthe pH adjusted to 5.0 with dilute sulfuric acid at 60° C. for threehours. Prior to incubation 0.05 GAU/g of glucoamylase was added.

Treatment 3 (Trt 3) is a room temperature treatment—a corn slurry wasobtained at room temperature prior to use in the fermentation with 0.5GAU glucoamylase/g of corn and 1.0 SSU/g corn of Tr-asaA.

Yeast fermentation was then carried out on each treatment as describedin example 7.

After the fermentation, ethanol yield was determined and the insolublesolids from each treatment were separated by centrifugation, dried at60° C. and the total carbohydrate content and nitrogen content weredetermined. The results are illustrated in Table 5, wherein Trt 3 is aprocess encompassed by the invention.

TABLE 5 Comparison of ethanol yield and the composition of DDGS ofdifferent treatments of whole ground corn substrate under ethanolfermentation using yeast Kgs % Residual % Total Corn Mash DDGS/MT starchcontent Protein Ethanol Treatment corn in DDGS in DDGS L/MT corn Trt 1326 4.8 27.5 402 High Temperature Trt 2 299 3.8 29.5 429 Low TemperatureTrt 3 274 3.5 31.6 438 No heat treatment GA + Tr-asaA

As observed from the results illustrated in Table 5, the % residualstarch in DDGS treated according to the process of the present invention(Trt 3) was less than the % residual starch obtained from the prior arttreatment (Trt 1) or the low temperature treatment (Trt 2). The valueswere 3.5% (Trt 3) as opposed to 4.8% or 3.8% for Trt1 and Trt 2. Thetotal protein content of the DDGS and the amount of ethanol produced washigher from Trt 3 according to the invention as compared to the priorart treatment (Trt 1).

Example 11 Incubation of Granular Corn Starch with Purified Aspergilluskawachi Alpha Amylase and Purified Aspergillus niger Glucoamylase EnzymePurification:

Aspergillus niger glucoamylase (GA) and Aspergillus kawachi alphaamylase (AkAA) were both purified from culture filtrate using apreparative high pressure liquid chromatographic (HPLC) method using anAKTA (Amersham Pharmacia, Biotech., NJ). In a typical experiment, bothcrude enzyme samples were desalted with 10 mM MES buffer (pH 5.75) tobring down the conductivity using a spin column (Bio-Rad, CA). Thesamples were brought up to 2M NH₄SO₂. The sample was loaded on to aQ-Sepharose column (Amersham, Biosciences, NJ) and eluted with 20 mM MESbuffer (pH 5.75) using a gradient of 1.5 M KCl. The fractions withcorresponding activity were pooled together and concentrated for furtherexperiments.

Incubation with Granular Corn Starch with Purified Enzymes:

The purified enzyme preparations were added to a 4.0% granular cornstarch (Cargill, Minneapolis, Minn.) in 0.1 M acetate buffer (pH 4.5) asfollows for Scanning Electron Microscopic (SEM) analysis.

Purified GA at 0.5 GAU/g corn starch; purified AkAA at 1.0 SSU/g starch;and GA and AkAA combined were incubated at 32° C. with gentle stirring.Aliquot samples (0.75 ml) were taken at intervals of 2, 4 and 8 hours,centrifuged and the soluble sugar determined by the method described inthe examples above. The pellet was resuspended in distilled water (5 ml)and centrifuged. The pellet was suspended again in 5 ml of absoluteethanol (99%), stirred for uniform mixing and centrifuged. The alcoholtreated pellet was air-dried in the tube and used for SEM analysis.

SEM Analysis:

Approximately 200 μl dry volume was transferred to a 1.5 ml Ependorftube and 0.8 ml absolute ethanol was added. The components were vortexedto make a suspension of starch particles. A few drops of suspension wasplaced on a freshly cleaned glass cover slip and allowed to air dry. Thecover slip was mounted on specimen stubs with carbon adhesive tabs,painted around the circumference with colloidal silver adhesive(Electron Microscopy Sciences, Ft. Washington, Pa.) and coated with athin layer of gold in a ScanCoat Six Sputter Coater (Edwards High VacuumIntl. Crawley, UK). Scanning electron microscopy was done at 5 kv in thesecondary electron imaging mode using a Quanta 200 FEG scanning electronmicroscope (FEI Inc., Hillsboro, Ore) at instrumental magnification of1,000 and 5,000×. Eight to ten images were made from different areas oneach sample stub. The effect of individual and combined enzymetreatments on the granular corn starch is illustrated in FIGS. 8 and 9.

Hydrolysis and Microscopic Examination:

Reducing sugar (mg/ml reducing equivalents), measured as glucosereleased after 4 hours as a result of granular starch hydrolysis by AkAAand GA is illustrated in FIG. 8. Degradation of granular starch withglucoamylase alone was 4.9 mg/ml; degradation of granular starch withAkM alone was only 0.3 mg/ml. However, degradation of granular starchwith the combination of GA and AkAA was 12.1 mg/ml. The degradationvalue for the enzymes combined illustrates a synergistic interaction,which is significantly greater than the additive value of the enzymes.

The starch granules treated as described in this example were observedwith a scanning electron microscope. As shown in FIG. 9, corn starchgranules incubated with purified AkAA did show minor surfacemodification. These were observed as small pin prick holes. Corn starchgranules incubated with purified GA showed many small defined deepholes. Significantly, corn starch granules incubated with thecombination of GA and AkAA showed numerous wide and deep penetratingcavities. Additionally, surface erosion, which exposed the layeredstructure of the granular center, was observed in the granules incubatedwith the combination of GA and AkAA.

Example 12 Effect of % Dry Solids Content (ds) of a Granular Corn StarchSlurry on Ethanol Yield

Corn flour was slurried with water to obtain a 36% ds mash. A smallamount of corn steep (0.2% of the slurry) was added along with 400 ppm(0.04%) urea to the mash prior to adjusting the pH to 4.5 with sulfuricacid. The dry solids content of the slurry was adjusted from 20 to 36%ds. The fermentations were carried out in 125 ml flasks containing atotal of 100 g mash. The enzymes were diluted so that a constant volumeof 0.5 ml was used for each enzyme. Each flask was inoculated with 3 mlof yeast that was propagated 17 hours prior to use. The yeastpropagation procedure involved adding 0.5% dry Fali yeast to 25% ds mashcontaining 0.5 GAU/g of GA and 1.5 SSU/g AkAA and incubating whilegently mixing in a 32° C. water bath. At approximately 24 hour timeintervals samples of beer were dried at 60° C. to obtain DDGS.

TABLE 6 Effect of DS Content on the Ethanol Production and ResidualStarch in DDGS at 75 hours AkAA (1.5 SSU/g ds) + GA (0.5 GAU/g ds) GA(0.5 GAU/g ds) DDGS DDGS % v/v % residual % v/v % residual % DS EtOHstarch EtOH starch 20 9.86 2.28 10.15 1.37 24 11.75 5.79 12.51 1.00 2813.51 13.07 14.80 1.83 32 15.38 18.06 17.47 3.78 36 16.39 29.37 18.0713.36

Almost all of the glucose (DP-1) generated during the fermentation wasconverted to ethanol except at the high solids (data not shown). Foreach % DS tested, the AkAA increased the rate and amount of ethanol.FIG. 10A summarizes the final ethanol level at each solids level andFIG. 10B shows the % increase in ethanol with AkAA for each solidagainst mash solids. Both figures demonstrate the positive effect AkAAhas on hydrolyzing granular starch and particularly at high solids %.Also as observed in FIG. 10A, as the dissolved solids increase, thedifference in the residual starch with and without AkAA also increases.As observed in FIG. 10B as the % ds in the corn slurry increases, theinfluence of AkAA on ethanol production increases.

The results from Table 6 and FIG. 11 clearly show a benefit of using acomposition of AkAA and GA in the methods of the invention. In allinstances the % starch in the DDGS is decreased when the AkAA is used incombination with the GA and further the % starch found in DDGS from acorn starch substrate having a % ds as high as 36% is reduced by halfwhen compared to the % starch in a DDGS without the addition of AkAA.

Example 13

A 33% slurry of corn flour (Azure Standard Farms) was prepared in DI H₂Oto which 400 ppm urea was added. The pH was adjusted to 5.0.Fermentation were conducted in 125 ml flasks containing 100 g mash andthe following treatments

A) A. niger GA blended with AkAA at 1.0 GAU/g and 3.0 SSU/g ds

B) HGA-GSHE at 1.0 GAU/g ds;

C) HGA-GSHE at 1.0 GAU/g and AkM at 3.0 SSU/g ds;

D) HGA-GSHE at 2.0 GAU/g ds and

E) HGA-GSHE at 2.0 GAU/g and AkAA at 3.0 SSU/g ds.

The enzymes were diluted so that 0.5 ml was added to each flask. A 3%slurry of Fali dry yeast in water was prepared and mixed with a 32° C.water bath one hour prior to inoculating the fermenters by adding 1.0 mlof the yeast slurry. The flasks were placed in a 32° C. water bath andthe mash mix gently. During the fermentations samples were removed forHPLC analysis. The fermentations were terminated after 72 hours and thebeer dried at 62° C. to obtain the DDGS. The starch content of the DDGSwas determined by the dual enzyme method.

TABLE 7 Total Sampled % w/v % v/v % v/v % Starch Treatment Hr LacticAcid Ethanol Ethanol DDGS A 22 0.07 10.69 10.77 A 46 0.08 18.02 18.07 A72 0.00 18.35 18.45 3.73 B 22 0.07 7.61 7.63 B 46 0.10 11.27 11.30 B 720.00 13.19 13.19 44.66 C 22 0.05 10.22 10.24 C 46 0.06 17.48 17.53 C 720.00 18.37 18.37 5.44 D 22 0.06 8.23 8.27 D 46 0.08 12.39 12.42 D 720.00 14.10 14.10 39.91 E 22 0.04 12.85 12.92 E 46 0.06 18.02 18.13 E 720.00 18.41 18.41 4.51

Example 14

A 33% slurry of corn flour (Azure Standard Farms) was prepared in DI H₂Oto which 400 ppm urea was added. The pH was adjusted to 4.5 with 5NH₂SO₄. Fermentation was conducted in 125 ml flasks containing 100 gmash. Enzymes as indicated below were diluted so that 0.5 ml was addedto each flask. A 3% slurry of Fali dry yeast in water was prepared andmixed with a 32° C. water bath one hour prior to inoculating thefermenters by adding 1.0 ml of the yeast slurry. The flasks were placedin a 32° C. water bath and the mash mix gently. During the fermentationssamples were removed for HPLC analysis. The fermentations wereterminated after 72 hours and the beer dried at 62° C. to obtain theDDGS. The starch content of the DDGS was determined

For table 8 below the enzyme treatments were 2.25 SSU AkAA and 0.75GAU/g ds of Aspergillus niger GA as DISTILLASE (AkAA/AnGA); 2.25 SSUAkAA and 0.72 GAU/g of HGA comprising the protein of SEQ ID NO: 13(AkAA/HGA) and 2.25 SSU AkAA and 1.6 GAU/g of TrGA comprising theprotein of SEQ ID NO: 12 (AkAA/TrGA).

TABLE 8 Sample Time % (v/v) Ethanol % (v/v) Ethanol % (v/v) Ethanol(hrs) AkAA/AnGA AkAA/TrGA AkAA/HGA 17 7.28 8.2 7.84 24 9.01 10.2 9.73 4814.07 14.89 14.28 72 15.85 16.39 16.11

Example 15

A 33% slurry of corn flour (Azure Standard Farms) was prepared in DI H₂O

To which 400 ppm urea was added. The pH was adjusted to 4.5 with5NH₂SO₄. Fermentation was conducted in 125 ml flasks containing 100 gmash. Enzymes as indicated below were diluted so that 0.5 ml was addedto each flask. A 3% slurry of Fali dry yeast in water was prepared andmixed with a 32° C. water bath one hour prior to inoculating thefermenters by adding 1.0 ml of the yeast slurry. The flasks were placedin a 32° C. water bath and the mash mix gently. During the fermentationssamples were removed for HPLC analysis at 22.5, 46 and 71 hours. Thefermentations were terminated after 71 hours. Aspergillus nigerglucoamylase was added to all flasks at 0.5 GAU/g. In addition, AkAAenzyme treatments including a) intact AkAA and b) the truncated AkAAenzymes of FIG. 5B, which were pooled together (see Example 5) weretested at different ratios of intact to truncated at a fixed AkAA dosagelevel of 1.5 SSU/g ds.

Increasing the ratio of intact to truncated AkAA gave increased ethanolproduction. At the end of the fermentation (71 hrs) the difference inethanol production was less pronounced than at 22.5 or 46 hours. Asobserved in FIG. 11, at 71 hours higher ethanol production occurred withtruncated AkAA as opposed to the control without AkAA. Furtherincreasing the amount of intact AkAA from 0 to 50% of the total leads toincreased ethanol production.

Example 16 Ethanol Production from Pullulanase in Combination withGlucoamylase and AkAA

A 36% corn flour slurry was prepared to which dry corn steep was addedat 2.5% of the corn weight. The pH of the slurry was adjusted to 4.8.The slurry was used for fermentation without any further treatment byplacing 100 gm of mash in 125 ml flasks. The desired amount of enzymeswere added to each flask as shown in Table 9, and the flasks were theninoculated with 3 ml of yeast that was propagated in the mash for 17hour. Each condition was run in duplicate.

The enzymes used were glucoamylase (GA) from a cell free culturefiltrate concentrated to 683 GAU/gm of enzyme by evaporation in a rotaryevaporator, AkAA at 5540 SSU/ml of enzyme, and pullulanase provided asOptimax L-1000

The flasks were placed in a 30° C. water bath and gently stirred with amagnetic stir bar. At various times, samples of the beer were removedfor HPLC analysis.

The fermentations were terminated after 72 hours. A portion of the beerwas dried at 60° C. to obtain the DDGS. The starch content of the DDGSswas then determined.

TABLE 9 GA - AkAA Ethanol Ethanol Ethanol % starch GAU/ SSU/ Pullulanase% v/v % v/v % v/v DDGS at g ds g ds ASPU/g 22 hrs 46 hrs 72 hrs 72 hrs0.5 1.0 0.0 10.73 16.80 19.16 4.02 0.5 1.0 0.5 11.15 17.52 19.20 3.530.5 1.0 1.0 11.38 17.63 19.10 4.67 0.5 1.0 2.0 11.63 18.15 19.46 4.15

As observed from Table 9, pullulanase increased the fermentation rateand gave a slight increase in ethanol. However, it did not appear thatpullulanase had an influence on the final ethanol yield at 72 hours. Inaddition % w/v was measured for DP>2, DP-2, DP-1, lactic acid andglycerol data not shown.

1. A method for the production of an end-product comprising contacting agranular starch substrate with an enzyme composition comprising an acidstable alpha amylase (asAA) having granular starch hydrolyzing (GSH)activity and at least 90% sequence identity to SEQ ID NO: 3 and anethanologenic microorganism under suitable fermentation conditions at atemperature between about 25 to 65° C. and producing an end-product. 2.The method according to claim 1, wherein the asAA having GSH activity isderived from the heterologous expression of the asAA in a filamentousfungal host cell.
 3. The method according to claim 2, wherein thefilamentous fungal host cell is a Trichoderma cell.
 4. The methodaccording to claim 1, wherein the contacting is at a temperature belowthe gelatinization temperature of the granular starch in the granularstarch substrate.
 5. The method according to claim 1, wherein thecontacting is at a temperature of between 25 and 45° C.
 6. The methodaccording to claim 5, wherein the contacting is at a temperature ofbetween 30 and 35° C.
 7. The method according to claim 1, wherein thecontacting is at a pH of about 3.5 to 5.5.
 8. The method according toclaim 1, wherein the contacting is for 2 to 120 hours.
 9. The methodaccording to claim 1 further comprising recovering the end-product. 10.The method according to claim 9, wherein the end-product is ethanol. 11.The method according to claim 10, wherein the amount of ethanol producedis at least about 10% v/v.
 12. The method according to claim 11, whereinthe amount of ethanol produced is at least 12% v/v.
 13. The methodaccording to claim 12 further comprising obtaining Distillers driedgrain plus solubles (DDGS) from the fermentation.
 14. The methodaccording to claim 13, wherein the DDGS comprises less than 15% residualstarch after 72 hours of fermentation.
 15. The method according to claim1, further comprising obtaining residual starch from the fermentationand recycling the residual starch for a second fermentation.
 16. Themethod according to claim 1, wherein the granular starch substrate is acereal grain or fractionated part thereof.
 17. The method according toclaim 16, wherein the cereal grain or fractionated part thereof isobtained from corn, wheat, rice, rye, barely sorghum.
 18. The methodaccording to claim 16, wherein the cereal grain is milled to a particlesize wherein at least 80% of the milled grain will pass through a 0.5 mmscreen.
 19. The method according to claim 1, wherein the asAA having GSHactivity has at least 95% sequence identity to SEQ ID NO: 3
 20. Themethod according to claim 19, wherein the asAA having GSH activity hasthe sequence of SEQ ID NO:
 3. 21. The method according to claim 1,wherein the enzyme compositions further includes a truncated asAA havingGSH activity.
 22. The method according to claim 21, wherein thetruncated asAA has at least 97% sequence identify to SEQ ID NO:
 9. 23.The method according to claim 1 further comprising contacting thegranular starch substrate with a glucoamylase.
 24. The method accordingto claim 23, wherein the glucoamylase is obtained from a filamentousfungal host.
 25. The method according to claim 24, wherein thefilamentous fungal host is selected from Aspergillus, Trichoderma,Humicola and Rhizopus strains.
 26. The method according to claim 1,wherein the ethanologenic microorganism is yeast.
 27. The methodaccording to claim 23, wherein the glucoamylase and asAA having GSHactivity are combined prior to the contacting.
 28. A method for theproduction of ethanol as an end-product comprising combining a granularstarch hydrolyzing composition comprising a) an acid stable alphaamylase (asAA) having granular starch hydrolyzing (GSH) activity and atleast 95% sequence identity to SEQ ID NO: 3 and b) a glucoamylase with agranular starch substrate and simultaneously fermenting the combinationwith an ethanologenic microorganism under suitable fermentationconditions which comprise a temperature of 25 to 45° C. and producingethanol.
 29. The method according to claim 28 further comprisingrecovering the ethanol.
 30. The method according to claim 28, whereinthe asAA having GSH activity is obtained from the heterologousexpression of asAA in a filamentous fungal host cell.
 31. The methodaccording to claim 30, wherein the filamentous fungal host cell is aTrichoderma cell.
 32. The method according to claim 28, wherein theglucoamylase is obtained from a filamentous fungus.
 33. The methodaccording to claim 32, wherein the filamentous fungus is a strain ofAspergillus, Trichoderma, Humicola or Rhizopus.
 34. The method accordingto claim 28, wherein the granular starch substrate is obtained from acereal grain or fractionated part thereof.
 35. The method according toclaim 28, wherein at least 50% of the starch solids from the granularstarch substrate are hydrolyzed after 2 to 100 hours.
 36. The methodaccording to claim 28, wherein the ratio of asAA to GA measured asweight is 10:1 to 1:10.
 37. The method according to claim 28, whereinthe granular starch substrate is corn having 25-45% dry solids content(ds).
 38. A method for reducing the residual starch content indistillers dried grains plus solids (DDGS) comprising producing analcohol according to the method of claim 23, separating the alcohol fromthe fermentation broth to obtain stillage, and converting the stillageto DDGS.
 39. The method according to claim 38, wherein the granularstarch substrate has a ds of about 25 to 40%.
 40. The method accordingto claim 38, wherein the residual starch content in the DDGS is lessthan 15%.
 41. The method according to claim 38, wherein the granularstarch substrate is from corn.